Method of screening for colorectal cancer

ABSTRACT

The present invention relates generally to a method of determining one or more probabilities of respective classifications of a neoplasm into one or more neoplastic categories. More particularly, the present invention relates to a method of determining the probability of classification of a large intestine neoplasm into one or more categories selected from adenoma, stage I, stage II, stage III or stage IV by screening for changes to the methylation levels of a panel of gene markers, including BCAT1, IKZF1, IRF4, GRASP and/or CAHM. The method of the present invention is useful in a range of applications including, but not limited to, those relating to the diagnosis and/or monitoring of colorectal neoplasms, such as colorectal adenocarcinosis.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.14/401,157, filed Nov. 14, 2014, which is a U.S. National PhaseApplication of PCT International Application Number PCT/AU2013/000519,filed on May 17, 2013, designating the United States of America andpublished in the English language, which is an International Applicationof and claims the benefit of priority to U.S. Provisional ApplicationNo. 61/648,821, filed May 18, 2012, the disclosures of which are herebyexpressly incorporated by reference in their entireties.

FIELD

The present invention relates generally to a method of classifying alarge intestine neoplasm and, in particular, classifying a colorectalneoplasm in a mammal. The present invention more specifically provides amethod for assessing the probability that a large intestine neoplasm isa premalignant neoplasm, an early stage malignant neoplasm or a latestage malignant neoplasm. The method of the present invention is basedon screening for modulation in the DNA methylation levels of one or moregene markers in blood samples from said mammal.

BACKGROUND

Colorectal cancer includes cancerous growths in the colon, rectum andappendix. With 655,000 deaths worldwide per year, it is the fourth mostcommon form of cancer in the United States, and the third leading causeof cancer-related deaths in the Western world. Colorectal cancers arisefrom adenomatous polyps in the colon. These mushroom-shaped growths areusually benign, but some develop into cancer over time. Localized coloncancer is usually diagnosed through colonoscopy.

Invasive cancers that are confined within the wall of the colon (Stage Iand II) are curable with surgery. If untreated, they spread to regionallymph nodes (stage III), where up to 73% are curable by surgery andchemotherapy. Cancer that metastasizes to distant sites (stage IV) isusually not curable, although chemotherapy can extend survival, and inrare cases, surgery and chemotherapy together have seen patients throughto a cure (Markowitz and Bertagnolli, 2009, N. Engl. J. Med. 361(25):2449-60). Radiation is used with rectal cancer.

Colorectal cancer is preceded by adenomas. Adenomas are benign tumours,or neoplasms, of epithelial origin which are derived from glandulartissue or exhibit clearly defined glandular structures. Some adenomasshow recognisable tissue elements, such as fibrous tissue(fibroadenomas) and epithelial structure, while others, such asbronchial adenomas, produce active compounds that might give rise toclinical syndromes.

Adenomas may progress to become an invasive neoplasm, and are thentermed adenocarcinomas. Accordingly, adenocarcinomas are defined asmalignant epithelial tumours arising from glandular structures, whichare constituent parts of many organs of the body. The termadenocarcinoma is also applied to tumours showing a glandular growthpattern. These tumours may be sub-classified according to the substancesthat they produce, for example mucus secreting and serousadenocarcinomas, or to the microscopic arrangement of their cells intopatterns, for example papillary and follicular adenocarcinomas. Thesecarcinomas may be solid or cystic (cystadenocarcinomas). Each organ mayproduce tumours showing a variety of histological types, for example theovary may produce both mucinous and cystadenocarcinoma.

Adenomas in different organs behave differently. In general, the overallchance of carcinoma being present within an adenoma (i.e., a focus ofcancer having developed within a benign lesion) is approximately 5%.However, this is related to size of an adenoma. For instance, in thelarge bowel (colon and rectum specifically), occurrence of a cancerwithin an adenoma is rare in adenomas of less than 1 centimetre. Such adevelopment is estimated at 40 to 50% in adenomas which are greater than4 centimetres and show certain histopathological change such as villouschange, or high grade dysplasia. Adenomas with higher degrees ofdysplasia have a higher incidence of carcinoma. In any given colorectaladenoma, the predictors of the presence of cancer now or the futureoccurrence of cancer in the organ include size (especially greater than9 mm), degree of change from tubular to villous morphology, presence ofhigh grade dysplasia and the morphological change described as “serratedadenoma”. In any given individual, the additional features of increasingage, familial occurrence of colorectal adenoma or cancer, male gender ormultiplicity of adenomas, predict a future increased risk for cancer inthe organ—so-called risk factors for cancer. Except for the presence ofadenomas and its size, none of these is objectively defined, and allthose other than number and size are subject to observer error and toconfusion as to precise definition of the feature in question. Becausesuch factors can be difficult to assess and define, their value aspredictors of current or future risk for cancer is imprecise.

Once a sporadic adenoma has developed, the chance of a new adenomaoccurring is approximately 30% within 26 months.

The symptoms of colorectal cancer depend on the location of tumour inthe bowel, and whether it has metastasised. Unfortunately, many of thesymptoms may occur in other diseases as well, and hence symptoms may notbe conclusively diagnostic of colorectal cancer.

Local symptoms are more likely if the tumour is located closer to theanus. There may be a change in bowel habit (new-onset constipation ordiarrhea in the absence of another cause), a feeling of incompletedefecation, and reduction in diameter of stools. Tenesmus and change instool shape are both characteristic of rectal cancer. Lowergastrointestinal bleeding, including the passage of bright red blood inthe stool, may indicate colorectal cancer, as may the increased presenceof mucus. Melena, black stool with a tarry appearance, normally occursin upper gastrointestinal bleeding (such as from a duodenal ulcer), butis sometimes encountered in colorectal cancer when the disease islocated in the beginning of the large bowel.

A tumour that is large enough to fill the entire lumen of the bowel maycause bowel obstruction. This situation is characterized byconstipation, abdominal pain, abdominal distension and vomiting. Thisoccasionally leads to the obstructed and distended bowel perforating andcausing peritonitis.

Certain local effects of colorectal cancer occur when the disease hasbecome more advanced. A large tumour is more likely to be noticed onfeeling the abdomen, and it may be noticed by a doctor on physicalexamination. The disease may invade other organs, and may cause blood orair in the urine or vaginal discharge.

If a tumour has caused chronic occult bleeding, iron deficiency anaemiamay occur. This may be experienced as fatigue, palpitations and noticedas pallor. Colorectal cancer may also lead to weight loss, generally dueto a decreased appetite.

More unusual constitutional symptoms are an unexplained fever and one ofseveral paraneoplastic syndromes. The most common paraneoplasticsyndrome is thrombosis, usually deep vein thrombosis.

Colorectal cancer most commonly spreads to the liver. This may gounnoticed, but large deposits in the liver may cause jaundice andabdominal pain (due to stretching of the capsule). If the tumour depositobstructs the bile duct, the jaundice may be accompanied by otherfeatures of biliary obstruction, such as pale stools.

Colorectal cancer can take many years to develop and early detection ofcolorectal cancer greatly improves the prognosis. Even modest efforts toimplement colorectal cancer screening methods can result in a drop incancer deaths. Despite this, colorectal cancer screening rates remainlow.

In addition to screening for the onset of a colorectal neoplasm,determining the stage or grade of a neoplasm is also extremely valuablesince this provides a patient with the possibility of better tailoredtreatment regimen and potentially a significantly better prognosis.Currently, staging of large intestine neoplasms is an invasive proceduresince it requires the harvesting of a tissue specimen which ishistologically analysed.

The most commonly used staging system for colorectal cancer is that ofthe American Joint Committee on Cancer (AJCC), sometimes also known asthe TNM system. The TNM system describes 3 key pieces of information:

T describes how far the main (primary) tumour has grown through thelayers of the intestine and whether it has grown into nearby areas.These layers, from the inner to the outer, include:

The inner lining (mucosa)

A thin muscle layer (muscularis mucosa)

The fibrous tissue beneath this muscle layer (submucosa)

A thick muscle layer (muscularis propria) that contracts to force thecontents of the intestines along

The thin, outermost layers of connective tissue (subserosa and serosa)that cover most of the colon but not the rectum

N describes the extent of spread to nearby (regional) lymph nodes, and,if so, how many lymph nodes are involved.

Nx: No description of lymph node involvement is possible because ofincomplete information.

N0: No cancer in nearby lymph nodes.

N1a: Cancer cells are found in 1 nearby lymph node.

N1b: Cancer cells are found in 2 to 3 nearby lymph nodes.

NU: Small deposits of cancer cells are found in areas of fat near lymphnodes, but not in the lymph nodes themselves.

N2a: Cancer cells are found in 4 to 6 nearby lymph nodes.

N2b: Cancer cells are found in 7 or more nearby lymph nodes.

M indicates whether the cancer has metastasized.

M0: No distant spread is seen.

M1a: The cancer has spread to 1 distant organ or set of distant lymphnodes.

M1b: The cancer has spread to more than 1 distant organ or set ofdistant lymph nodes, or it has spread to distant parts of the peritoneum(the lining of the abdominal cavity).

Numbers or letters appear after T, N, and M to provide more detailsabout each of these factors. The numbers 0 through 4 indicate increasingseverity. The letter X means “cannot be assessed because the informationis not available.”

T Categories for Colorectal Cancer

T categories of colorectal cancer describe the extent of spread throughthe layers that form the wall of the colon and rectum.

Stage Grouping

Once a person's T, N, and M categories have been determined, usuallyafter surgery, this information is combined in a process called stagegrouping. The stage is expressed in Roman numerals from stage I (theleast advanced) to stage IV (the most advanced). Some stages aresubdivided with letters.

Stage 0

Tis, N0, M0: The cancer is in the earliest stage. It has not grownbeyond the inner layer (mucosa) of the colon or rectum. This stage isalso known as carcinoma in situ or intramucosal carcinoma.

Stage I

T1-T2, N0, M0: The cancer has grown through the muscularis mucosa intothe submucosa (T1) or it may also have grown into the muscularis propria(T2). It has not spread to nearby lymph nodes or distant sites.

Stage IIA

T3, N0, M0: The cancer has grown into the outermost layers of the colonor rectum but has not gone through them. It has not reached nearbyorgans. It has not yet spread to the nearby lymph nodes or distantsites.

Stage IIB

T4a, N0, M0: The cancer has grown through the wall of the colon orrectum but has not grown into other nearby tissues or organs. It has notyet spread to the nearby lymph nodes or distant sites.

Stage IIC

T4b, N0, M0: The cancer has grown through the wall of the colon orrectum and is attached to or has grown into other nearby tissues ororgans. It has not yet spread to the nearby lymph nodes or distantsites.

Stage IIIA

One of the following applies.

T1-T2, N1, M0: The cancer has grown through the mucosa into thesubmucosa (T1) or it may also have grown into the muscularis propria(T2). It has spread to 1 to 3 nearby lymph nodes (N1a/N1b) or into areasof fat near the lymph nodes but not the nodes themselves (N1c). It hasnot spread to distant sites.

T1, N2a, M0: The cancer has grown through the mucosa into the submucosa.

It has spread to 4 to 6 nearby lymph nodes. It has not spread to distantsites.

Stage IIIB

One of the following applies.

T3-T4a, N1, M0: The cancer has grown into the outermost layers of thecolon or rectum (T3) or through the visceral peritoneum (T4a) but hasnot reached nearby organs. It has spread to 1 to 3 nearby lymph nodes(N1a/N1b) or into areas of fat near the lymph nodes but not the nodesthemselves (N1c). It has not spread to distant sites.

T2-T3, N2a, M0: The cancer has grown into the muscularis propria (T2) orinto the outermost layers of the colon or rectum (T3). It has spread to4 to 6 nearby lymph nodes. It has not spread to distant sites.

T1-T2, N2b, M0: The cancer has grown through the mucosa into thesubmucosa (T1) or it may also have grown into the muscularis propria(T2). It has spread to 7 or more nearby lymph nodes. It has not spreadto distant sites.

Stage IIIC

One of the following applies.

T4a, N2a, M0: The cancer has grown through the wall of the colon orrectum (including the visceral peritoneum) but has not reached nearbyorgans. It has spread to 4 to 6 nearby lymph nodes. It has not spread todistant sites.

T3-T4a, N2b, M0: The cancer has grown into the outermost layers of thecolon or rectum (T3) or through the visceral peritoneum (T4a) but hasnot reached nearby organs. It has spread to 7 or more nearby lymphnodes. It has not spread to distant sites.

T4b, N1-N2, M0: The cancer has grown through the wall of the colon orrectum and is attached to or has grown into other nearby tissues ororgans. It has spread to 1 or more nearby lymph nodes or into areas offat near the lymph nodes. It has not spread to distant sites.

Stage IVA

Any T, Any N, M1a: The cancer may or may not have grown through the wallof the colon or rectum, and it may or may not have spread to nearbylymph nodes. It has spread to 1 distant organ (such as the liver orlung) or set of lymph nodes.

Stage IVB

Any T, Any N, M1b: The cancer may or may not have grown through the wallof the colon or rectum, and it may or may not have spread to nearbylymph nodes. It has spread to more than 1 distant organ (such as theliver or lung) or set of lymph nodes, or it has spread to distant partsof the peritoneum (the lining of the abdominal cavity).

Another factor that can affect the outlook for survival is the grade ofthe cancer. Grade is a description of how closely the cancer resemblesnormal colorectal tissue when looked at under a microscope.

The scale used for grading colorectal cancers goes from G1 (where thecancer looks much like normal colorectal tissue) to G4 (where the cancerlooks very abnormal). The grades G2 and G3 fall somewhere in between.The grade is often simplified as either “low-grade” (G1 or G2) or“high-grade” (G3 or G4). Low-grade cancers tend to grow and spread moreslowly than high-grade cancers.

In the context of large intestine neoplasms, the histological analysisof tissue specimens is both relatively slow and highly invasive. Due toits invasiveness, it is also not a procedure which one would want toperform repeatedly. The development of a means to reliably and routinelyassess a patient to determine whether an identified neoplasm ispremalignant (e.g., adenoma), early stage or late stage (e.g.,metastatic) is highly desirable if it can be performed quickly andrepeatedly, since this would enable decisions in relation to treatmentregimes to be made and implemented more accurately. It would also enableongoing monitoring to be performed during a treatment regime, such as inthe context of treating an adenoma or early stage cancer, to assesstransition to a more advanced stage without the need to perform invasivebiopsies. This would also enable more flexibility in terms of adaptingtreatment regimes to reflect changes to the stage of a neoplasm.

In work leading up to the present invention, it has been determined thata panel of gene markers which are known to be diagnostic of largeintestine neoplasms can, in fact, also provide valuable information inrelation to the classification of a neoplasm. Specifically, whereas thelevel of increase in the methylation of the DNA of these gene markers issimilar in most biological samples, irrespective of how advanced theneoplasm is, when assessed in a blood-derived sample, such as plasma,there is found an increase in the level of methylation as the stage ofthe neoplasm becomes more advanced.

This finding has therefore now provided a means to assess theprobability that a given neoplasm is premalignant, early stagemalignant, or late stage malignant. This information in relation to theclassification of the neoplasm can then inform the development of thetherapeutic treatment and ongoing monitoring which is appropriate forthe patient. Importantly, particularly in the context of premalignant orearly stage malignant neoplasms, it provides a means for non-invasiveongoing monitoring. The method of the present invention can be performedeither after initial diagnosis, or may itself form part of the screeningof patients presenting for initial diagnosis but where, in addition tothe diagnostic result, there is also provided classificationinformation.

SUMMARY

Throughout this specification and the claims which follow, unless thecontext requires otherwise, the word “comprise”, and variations such as“comprises” and “comprising”, will be understood to imply the inclusionof a stated integer or step or group of integers or steps but not theexclusion of any other integer or step or group of integers or steps.

As used herein, the term “derived from” shall be taken to indicate thata particular integer or group of integers has originated from thespecies specified, but has not necessarily been obtained directly fromthe specified source. Further, as used herein the singular forms of “a”,“and” and “the” include plural referents unless the context clearlydictates otherwise.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs.

The subject specification contains nucleotide sequence informationprepared using the programme PatentIn Version 3.5, presented hereinafter the bibliography. Each nucleotide sequence is identified in thesequence listing by the numeric indicator <210> followed by the sequenceidentifier (eg. <210>1, <210>2, etc). The length, type of sequence (DNA,etc) and source organism for each sequence is indicated by informationprovided in the numeric indicator fields <211>, <212> and <213>,respectively. Nucleotide sequences referred to in the specification areidentified by the indicator SEQ ID NO: followed by the sequenceidentifier (eg. SEQ ID NO:1, SEQ ID NO:2, etc.). The sequence identifierreferred to in the specification correlates to the information providedin numeric indicator field <400> in the sequence listing, which isfollowed by the sequence identifier (eg. <400>1, <400>2, etc). That isSEQ ID NO:1 as detailed in the specification correlates to the sequenceindicated as <400>1 in the sequence listing.

A method of determining one or more probabilities of respectiveclassifications of a large intestine neoplasm in an individual, saidmethod comprising assessing the methylation status of a DNA regionselected from:

-   (i) the region, including 2 kb upstream of the transcription start    site, defined by at least one of Hg19 coordinates:    -   (1) chr12:24962958..25102393    -   (2) chr7:50344378 . . . 50472798    -   (3) chr6:391739..411443;    -   (4) chr12:52400748..52409671; and    -   (5) chr6:163834097..163834982; or-   (ii) the gene region, including 2 kb upstream of at least one of:

(1) BCAT1 (2) IKZF1 (3) IRF4 (4) GRASP and (5) CAHM

in a blood-derived sample from said individual, wherein a level ofmethylation of at least one of the DNA regions of group (i) and/or (ii)relative to corresponding measured levels of methylation from apopulation of individuals with known neoplastic categories ofcorresponding large intestine neoplasms is used to determine one or moreprobabilities of respective classifications of said large intestineneoplasm of said individual into one or more neoplastic categoriesselected from adenoma, stage I, stage II, stage III, and stage IVcategories or into one or more aggregates of fewer than five of saidneoplastic categories.

In one embodiment, the method is directed to determining one or moreprobabilities of respective classifications of said large intestineneoplasms of said individual into one or more aggregates of fewer thanfive of said neoplastic categories.

The method may further include using said level of methylation for saidindividual to determine a probability that said large intestine of saidindividual would be classified as non-neoplastic, based on comparison ofsaid level of methylation relative to said corresponding measured levelsof methylation and to further corresponding measured levels ofmethylation from a further population of individuals whose largeintestines were classified as non-neoplastic.

The subregions which have been determined to exhibit particular utilityare listed below with reference to the gene and chromosomal regionwithin which they are found:

-   (1) BCAT1 subregions chr12:25101992-25102093 (SEQ ID NO:1 or the    corresponding minus strand) and chr12:25101909-25101995 (SEQ ID NO:2    or the corresponding minus strand)-   (2) IKZF1 subregions: chr7:50343867-50343961 (SEQ ID NO:3 or the    corresponding minus strand) and chr7:50343804-5033895 (SEQ ID NO:4    or the corresponding minus strand)-   (3) IRF4 subregions chr6:392036-392145 (SEQ ID NO:5 or the    corresponding minus strand)-   (4) GRASP subregions: chr12:52399672-52399922,    chr12:52400821-52401051 (SEQ ID NO:6 or the corresponding minus    strand), chr12:52401407-52401664 (SEQ ID NO:7 or the corresponding    minus strand) chr12:52400866-52400973 and Chr12:52401107-52401664.-   (5) CAHM subregions: chr6:163834295-163834500 (SEQ ID NO:8 or the    corresponding minus strand), chr6:163834621-163834906    chr6:163834393-163834455 and chr6: 163834393-163834519.

Without limiting the present invention to any one theory or mode ofaction, the skilled person may screen one or more subregions for eachgene marker.

To the extent that the method of the present invention includesanalysing the methylation of BCAT1, the subject residues:

chr12: 25101998 chr12: 25102003 chr12: 25102006 chr12: 25102009 chr12:25102017 chr12: 25102022 chr12: 25102039 chr12: 25102048 chr12: 25102050chr12: 25102053 chr12: 25102061 chr12: 25102063 chr12: 25102071 chrl12:25101921 chr12: 25101934 chr12: 25101943 chr12: 25101951 chr12: 25101962chr12: 25101964 chr12: 25101970or a corresponding cytosine at position n+1 on the opposite DNA strand.

To the extent that the method of the present invention includesanalysing the methylation of GRASP, the subject residues are:

chr12: 52399713 chr12: 52399731 chr12: 52399749 chr12: 52399783 chr12:52399796 chr12: 52399808 chr12: 52399823 chr12: 52399835 chr12: 52399891chr12: 52400847 chr12: 52400850 chr12: 52400859 chr12: 52400866 chr12:52400869 chr12: 52400873 chr12: 52400881 chr12: 52400886 chr12: 52400893chr12: 52400895 chr12: 52400899 chr12: 52400902 chr12: 52400907 chr12:52400913 chr12: 52400919 chr12: 52400932 chr12: 52400938 chr12: 52400958chr12: 52400962 chr12: 52400971 chr12: 52400973 chr12: 52400976 chr12:52400998 chr12: 52401008 chr12: 52401010 chr12: 52401012 chr12: 52401016chr12: 52401019 chr12: 52401025 chr12: 52401041 chr12: 52401044 chr12:52401053 chr12: 52401060 chr12: 52401064 chr12: 52401092 chr12: 52401118chr12: 52401438 chr12: 52401448 chr12: 52401460 chr12: 52401465 chr12:52401474 chr12: 52401477 chr12: 52401479 chr12: 52401483 chr12: 52401504chr12: 52401514 chr12: 52401523 chr12: 52401540 chr12: 52401553 chr12:52401576 chr12: 52401588 chr12: 52401595 chr12: 52401599 chr12: 52401604chr12: 52401606 chr12: 52401634 chr12: 52401640 chr12: 52401644 chr12:52401659 chr12: 52401160 chr12: 52401165 chr12: 52401174 chr12: 52401177chr12: 52401179 chr12: 52401183 chr12: 52401204 chr12: 52401215 chr12:52401223 chr12: 52401240 chr12: 52401253 chr12: 52401288 chr12: 52401295chr12: 52401299 chr12: 52401304 chr12: 52401334 chr12: 52401340 chr12:52401344 chr12: 52401359or a corresponding cytosine at position n+1 on the opposite DNA strand.

To the extent that the method of the present invention includesanalysing the methylation of CAHM, the subject residues are:

chr6: 163834330 chr6: 163834332 chr6: 163834357 chr6: 163834373 chr6:163834384 chr6: 163834390 chr6: 163834392 chr6: 163834406 chr6:163834412 chr6: 163834419 chr6: 163834443 chr6: 163834448 chr6:163834452 chr6: 163834464 chr6: 163834483 chr6: 163834653 chr6:163834660 chr6: 163834672 chr6: 163834675 chr6: 163834678 chr6:163834681 chr6: 163834815 chr6: 163834824 chr6: 163834835 chr6:163834840 chr6: 163834853 chr6: 163834855 chr6: 163834858 chr6:163834863 chr6: 163834869 chr6: 163834872or a corresponding cytosine at position n+1 on the opposite DNA strand.

To the extent that the method of the present invention includesanalysing the methylation of IKZF1, the subject residues are:

chr7: 50343869 chr7: 50343872 chr7: 50343883 chr7: 50343889 chr7:50343890 chr7: 50343897 chr7: 50343907 chr7: 50343909 chr7: 50343914chr7: 50343934 chr7: 50343939 chr7: 50343950 chr7: 50343959 chr7:50343805 chr7: 50343822 chr7: 50343824 chr7: 50343826 chr7: 50343829chr7: 50343831 chr7: 50343833 chr7: 50343838 chr7: 50343847 chr7:50343850 chr7: 50343858 chr7: 50343864 chr7: 50343869 chr7: 50343872chr7: 50343890or a corresponding cytosine at position n+1 on the opposite DNA strand.

To the extent that the method of the present invention includesanalysing the methylation of IRF4, the subject residues are:

chr6: 392036 chr6: 392047 chr6: 392049 chr6: 392057 chr6: 392060 chr6:392066 chr6: 392080 chr6: 392094 chr6: 392102 chr6: 392131or a corresponding cytosine at position n+1 on the opposite DNA strand.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Measurement of CAHM methylation levels in tissue and bloodplasma specimens. A: The levels of methylated CAHM in colorectal tissuespecimens including normals (n=26, solid circles), adenomas (n=17, solidsquares), Stage 1 (n=20, open squares), Stage II (n=21, open circles),Stage III (n=30, open diamonds) and Stage IV (n=8, crosses) weremeasured using the methylation specific CAHM assay described in M&M on15 ng of bisulfite converted DNA extracted from 122 tissue specimens(Left figure). The signal output was converted to a mass/well using acalibration curve. Data is given as the % methylated CAHM measured in 15ng of total bisulfite converted tissue DNA per reaction. Data are meanvalues of triplicate. B: The levels of methylated CAHM was measured inthe equivalent of triplicate analysis of 0.5 mL plasma fromcolonoscopy-confirmed patients including normals (n=74, solid circles),adenomas (n=73, solid squares), Stage 1 (n=12, open squares), Stage II(n=21, open circles), Stage III (n=23, open diamonds) and Stage IV(n=12, black crosses). The signal output was converted to a mass using acalibration curve. Data is given as pg methylated CAHM per mL plasma.Data are mean values of triplicate. Increased masses of methylated CAHMwas observed in blood plasma from patients as a function of diseaseprogression (i.e. pg/mL CAHM was calculated to be higher in Stage III-IVcompared Stage I-II). In contrast, high and similar levels of pgmethylated CAHM was measured in colorectal tissue from the earliestonset of disease (precancerous) to late stage cancer. C: The levels ofmethylated CAHM was measured and plotted in a scatter graph of pgmethylated CAHM/ml plasma (log 10) vs. wt DNA ng/mL plasma fromcolonoscopy-confirmed patients including normal (n=74, solid circles),adenomas (n=73, solid squares), Stage I (n=12, open squares), Stage II(n=21, open circles), Stage III (n=23, open diamonds) and Stage IV(n=12, black crosses).

FIG. 2. Increased levels of methylated colorectal cancer biomarkers inblood plasma as a function of disease progression. Measurement of CAHMmethylation levels in tissue and blood plasma specimens. The levels ofmethylated IRF4 (A), GRASP (B), BCAT1 (C) and IKZF1 (D) were measured inthe equivalent of triplicate analysis of 0.5 mL plasma fromcolonoscopy-confirmed patients including normals (solid circles),adenomas (solid squares), Stage 1 (open squares), Stage II (opencircles), Stage III (open diamonds) and Stage IV (crosses). The signaloutput was converted to a mass/well using a calibration curve. Data isgiven as pg methylated biomarker per mL plasma. Data are mean values oftriplicate. As exemplified in FIG. 1 for CAHM, FIG. 2 demonstratesanother four biomarkers, namely, GRASP, IRF4, BCAT1 and IKZF1, wheremeasurement of blood plasma methylation levels may be indicative ofcolorectal cancer progression.

FIGS. 3A and 3B. Density distributions of methylated CAHM grouped byphenotype classification estimated from assay determined methylationlevels. FIG. 3A) Empirical probability density curves for CAHM based onmethylation levels previously determined by methylated CAHM assays (cfFIG. 1B). Density is estimated using only positive assay values fornon-neoplastic plasma specimens (black); premalignant adenomas (blue);early stage cancers including plasma from patients diagnosed with Stage1 or Stage 2 (red); and late stage cancers including plasma frompatients diagnosed with Stage 3 or Stage 4 (purple). FIG. 3B) Estimatednormal (Gaussian) distribution using mean and standard deviationestimates determined from positive methylation levels measured in plasmadrawn from patients with premalignant neoplastic lesions (blue); earlystage cancers (red) and late stage cancers (purple).

DETAILED DESCRIPTION

The present invention is predicated, in part, on the determination thatseveral genes which are known to exhibit increased levels of methylationin individuals exhibiting large intestine neoplasms are also anindicator of the classification of the neoplasm. Specifically, it hasbeen surprisingly determined that although the relative increase in DNAmethylation levels of a given gene marker is relatively consistent in atissue biopsy irrespective of the stage or grade of the neoplasm inissue, the same is not true if a blood-derived sample, such as plasma,is analysed. In particular, whereas a blood-derived sample will alsoshow increased levels of DNA methylation in the context of the presenceof a large intestine malignancy, these increased methylation levelsbecome progressively more increased as the malignancy becomes moreadvanced. This is not observed in tissue specimens. Accordingly, byassessing DNA methylation levels in accordance with the method of thepresent invention, one can determine not only whether or not malignanttransformation has occurred, but further the likely probability that themalignancy would be classified as early stage or late stage.

Accordingly, one aspect of the present invention is directed to a methodof determining one or more probabilities of respective classificationsof a large intestine neoplasm in an individual, said method comprisingassessing the methylation status of a DNA region selected from:

-   (i) the region, including 2 kb upstream of the transcription start    site, defined by at least one of Hg19 coordinates:    -   (1) chr12:24962958..25102393    -   (2) chr7:50344378 . . . 50472798    -   (3) chr6:391739..411443;    -   (4) chr12:52400748..52409671; and    -   (5) chr6:163834097..163834982; or-   (ii) the gene region, including 2 kb upstream of at least one of:

(1) BCAT1 (2) IKZF1 (3) IRF4 (4) GRASP and (5) CAHM

in a blood-derived sample from said individual, wherein a level ofmethylation of at least one of the DNA regions of group (i) and/or (ii)relative to corresponding measured levels of methylation from apopulation of individuals with known neoplastic categories ofcorresponding large intestine neoplasms is used to determine one or moreprobabilities of respective classifications of said large intestineneoplasm of said individual into one or more neoplastic categoriesselected from adenoma, stage I, stage II, stage III, and stage IVcategories or into one or more aggregates of fewer than five of saidneoplastic categories.

In one embodiment, the method is directed to determining one or moreprobabilities of respective classifications of said large intestineneoplasms of said individual into one or more aggregates of fewer thanfive of said neoplastic categories.

The method may further include using said level of methylation for saidindividual to determine a probability that said large intestine of saidindividual would be classified as non-neoplastic, based on comparison ofsaid level of methylation relative to said corresponding measured levelsof methylation and to further corresponding measured levels ofmethylation from a further population of individuals whose largeintestines were classified as non-neoplastic.

The aggregate categories may include one or more aggregates of fewerthan five of said neoplastic categories and an aggregate of thenon-neoplastic category with at least the adenoma category.

The aggregate categories may include a pre-malignant neoplasm categoryconsisting of an aggregate of the non-neoplastic and adenoma categories.

The aggregate categories may include an early stage malignant neoplasmcategory consisting of an aggregate of the stage I and stage IIcategories.

The aggregate categories may include a late stage malignant neoplasmcategory consisting of an aggregate of the stage III and stage IVcategories.

The aggregate categories may include the pre-malignant neoplasmcategory, early stage malignant neoplasm category, and late stagemalignant neoplasm categories.

Given measured levels of methylation in a population of individuals withknown classifications of large intestine neoplasms into neoplasticcategories selected from adenoma, stage I, stage II, stage III, andstage IV categories or aggregates of fewer than five of said neoplasticcategories, and further measured levels of methylation in a furtherpopulation of individuals whose large intestines were classified asnon-neoplastic, the prior statistical relationships between the measuredmethylation levels and the corresponding known categories for thepopulations of individuals can be used to determine one or moreprobabilities that a further measured methylation level of an individualcorresponds to respective ones of the same categories of the largeintestine neoplasm or non-neoplastic large intestine of said individual.As will be apparent to those skilled in the art, the determination canbe made using any one of a variety of standard statistical methods,including Bayesian statistics and machine learning.

In some embodiments, the statistical method includes generatinghistograms wherein the measured levels of methylation corresponding toknown categories are allocated into bins of respective ranges ofmethylation levels and using these histograms to estimate at least oneprobability that a further measured methylation level corresponds to atleast one of the known categories. As will be apparent to those skilledin the art, there are many methods to estimate classificationprobabilities. For example, by adding the total sizes of the binscorresponding to methylation levels of equal or lesser levels to themethylation level in question and dividing this sum by the total acrossall bins, one can estimate the proportion of methylation levels at orbelow a given level which are of a known category and thus theprobability that a measured methylation level is of said category.

In some embodiments, the statistical distributions of said measuredlevels of methylation are modelled by standard statistical distributionssuch as a Gaussian distribution, for example, and a standard fitting orregression procedure such as maximum likelihood is used to determine theparameters of the distributions, which can then be applied to a furthermeasured level of methylation from an individual to determine one ormore probabilities that the large intestine of that individual would beclassified as respective ones of the neoplastic categories and thenon-neoplastic category.

In some embodiments, the method may include using the determinedprobabilities to automatically classify the large intestine neoplasm ofthe individual into one of the prior known classifications, whetherneoplastic or non-neoplastic. However, given the overlap betweenmeasured levels of methylation for the different categories, theprobabilities are generally more useful for the selection of possiblefurther medical treatment options.

In other embodiments, the statistical associations between the measuredmethylation levels on the one hand and the corresponding categoriesobserved by colonoscopy or surgery on the other are used as a trainingset for supervised learning. The resulting weights are then applied toat least one further measured methylation level for at least one furtherindividual in order to determine corresponding probabilities formembership of those categories for that at least one individual. As willbe apparent to those skilled in the art, any one of a number of standardsupervised training methods can be used.

The categories used for supervised learning may include all fiveneoplastic categories and the non-neoplastic category, or aggregates ofthose six categories, such as the aggregate categories described above.The selection of which categories to use for supervised training may bebased on diagnostic/treatment requirements and/or the available numberand/or classification confidence of the observed categories (e.g., inorder to improve sensitivity and specificity of classification). In anycase, the weights generated by supervised learning can also be providedas inputs to a standard classifier in order to classify the largeintestine of the individual into a neoplastic or non-neoplastic class orcategory based on the corresponding measured methylation level.

Reference to “neoplasm” should be understood as a reference to a lesion,tumour or other encapsulated or unencapsulated mass or other form ofgrowth which comprises neoplastic cells. A ‘neoplastic cell” should beunderstood as a reference to a cell exhibiting abnormal growth. The term“growth” should be understood in its broadest sense and includesreference to proliferation. In this regard, an example of abnormal cellgrowth is the uncontrolled proliferation of a cell. Another example isfailed apoptosis in a cell, thus prolonging its usual life span. Theneoplastic cell may be a benign cell or a malignant cell. In a preferredembodiment, the subject neoplasm is an adenoma or an adenocarcinoma.Without limiting the present invention to any one theory or mode ofaction, an adenoma is generally a benign tumour of epithelial originwhich is either derived from epithelial tissue or exhibits clearlydefined epithelial structures. These structures may take on a glandularappearance. It can comprise a malignant cell population within theadenoma, such as occurs with the progression of a benign adenoma orbenign neoplastic legion to a malignant adenocarcinoma.

Reference to “large intestine” should be understood as a reference to acell derived from one of the eight anatomical regions of the largeintestine, which regions commence after the terminal region of theileum, these being:

(i) the cecum;

(ii) the ascending colon;

(iii) the transverse colon;

(iv) the descending colon;

(v) the sigmoid colon;

(vi) the rectum;

(vii) the splenic flexure; and

(viii) the hepatic flexure.

Preferably, said neoplastic cell is an adenoma or adenocarcinoma andeven more preferably a colorectal adenoma or adenocarcinoma.

Reference to “DNA region” should be understood as a reference to aspecific section of genomic DNA. These DNA regions are specified eitherby reference to a gene name or a set of chromosomal coordinates. Boththe gene names and the chromosomal coordinates would be well known to,and understood by, the person of skill in the art. As detailedhereinbefore, the chromosomal coordinates correspond to the Hg19 versionof the genome. In general, a gene can be routinely identified byreference to its name, via which both its sequences and chromosomallocation can be routinely obtained, or by reference to its chromosomalcoordinates, via which both the gene name and its sequence can also beroutinely obtained.

Reference to each of the genes/DNA regions detailed above should beunderstood as a reference to all forms of these molecules and tofragments or variants thereof. As would be appreciated by the person ofskill in the art, some genes are known to exhibit allelic variationbetween individuals or single nucleotide polymorphisms. SNPs encompassinsertions and deletions of varying size and simple sequence repeats,such as dinucleotide and trinucleotide repeats. Variants include nucleicacid sequences from the same region sharing at least 90%, 95%, 98%, 99%sequence identity i.e. having one or more deletions, additions,substitutions, inverted sequences etc. relative to the DNA regionsdescribed herein. Accordingly, the present invention should beunderstood to extend to such variants which, in terms of the presentdiagnostic applications, achieve the same outcome despite the fact thatminor genetic variations between the actual nucleic acid sequences mayexist between individuals. The present invention should therefore beunderstood to extend to all forms of DNA which arise from any othermutation, polymorphic or allelic variation.

It should be understood that the “individual” who is the subject oftesting may be any human or non-human mammal. Examples of non-humanmammals includes primates, livestock animals (e.g. horses, cattle,sheep, pigs, donkeys), laboratory test animals (e.g. mice, rats,rabbits, guinea pigs), companion animals (e.g. dogs, cats) and captivewild animals (e.g. deer, foxes).

Preferably, said mammal is a human.

As detailed hereinbefore, the method of the present invention enablesone to assess the probability that a neoplasm is a premalignantneoplasm, early stage malignancy or late stage malignancy. Although thestaging and grading systems which are commonly used by pathologists inthe context of large intestine neoplasms (such as colorectal cancers)can purportedly stage such cancers quite precisely, the fact is thatthey require a biopsy specimen to be harvested, this being a procedurewhich is invasive. Since the assessment required to be performed is thepreparation and histological analysis of a tissue section, it can alsotake some time to obtain results. In terms of accurately assessinghistological specimens, the interpretation of the sections is subjectiveand can be extremely difficult and unreliable, particularly in thecontext of moderate grade cancers, as opposed to very early stagecancers or metastatic cancers. Accordingly, the identification of amolecular basis upon which to classify a neoplasm is a significantadvance due to the fact that such analyses are not subjective. Stillfurther, since the DNA methylation levels of the genes at issue areassessed in a blood sample, this is the first available non-invasivemeans of classifying a large intestine neoplasm.

Without limiting the present invention to any one theory or mode ofaction, the most commonly used staging system for colorectal cancer isthat of the American Joint Committee on Cancer (AJCC), sometimes alsoknown as the TNM system. The TNM system describes 3 key pieces ofinformation:

T describes how far the main (primary) tumour has grown into the wall ofthe intestine and whether it has grown into nearby areas.

N describes the extent of spread to nearby (regional) lymph nodes.

M indicates whether the cancer has metastasized.

Numbers or letters appear after T, N, and M to provide more detailsabout each of these factors. The numbers 0 through 4 indicate increasingseverity.

A detailed description in relation to how the TNM system is applied hasbeen detailed earlier.

Once a person's T, N, and M categories have been determined, usuallyafter surgery, this information is combined in a process called stagegrouping. The stage is expressed in Roman numerals from stage I (theleast advanced) to stage IV (the most advanced). Nevertheless, despitethe apparent theoretical precision with which staging parameters areclassified, the reality in terms of assessing these parameters is farless precise. The present method has enabled a simpler and more reliablestaging system to be made available. Specifically, a patient is assessedto determine the probability that a neoplasm is a “premalignantneoplasm”, “early stage malignant neoplasm” or “late stage malignantneoplasm”. Based on these results, one may elect to also have a biopsyor some other diagnostic procedure performed. Alternatively one may usethese results to inform what therapeutic or palliative care regimeshould be designed and implemented. Of particular advantage is the factthat this method enables ongoing testing to be performed. This may beparticularly relevant where a premalignant neoplasm has been identifiedand a decision has been made not to surgically remove the neoplasm inthe first instance but to attempt to treat it.

In the context of the present invention, reference to “premalignantneoplasm” should be understood as a reference to a neoplasm which is notmalignant. An example of a non-malignant neoplasm is an adenoma. Withoutlimiting the present invention in any way, the histological andfunctional characteristics of a premalignant large intestine neoplasmare evidence of new, abnormal tissue growth without evidence ofinvasion.

Reference to an “early stage malignant neoplasm” is a reference to alarge intestine neoplasm which has become malignant but which isunlikely to extend beyond the bowel wall.

Reference to a “late stage malignant neoplasm” should be understood as areference to a large intestine neoplasm which is malignant and which hasspread to lymph nodes or distant organs. Reference to late stagemalignant neoplasms includes, for example, neoplasms which have becomemetastatic.

In terms of screening for the methylation of these gene regions, itshould be understood that the assays can be designed to screen eitherthe specific regions listed herein (which correspond to the “plus”strand of the gene) or the complementary “minus” strand. It is wellwithin the skill of the person in the art to choose which strand toanalyse and to target that strand based on the chromosomal coordinatesprovided herein. In some circumstances, assays may be established toscreen both strands.

Without limiting the present invention to any one theory or mode ofaction, although measuring the methylation levels across these DNAregions is diagnostic of the classification of a large intestineneoplastic condition, it has been determined that discrete subregionsare particularly useful in this regard since these subregions contain ahigh density of CpG dinucleotides which are frequently hypermethylatedin large intestine neoplasias, such as colorectal cancers. This findingrenders these subregions a particularly useful target for analysis sinceit both simplifies the screening process due to a shorter more clearlydefined region of DNA requiring analysis and, further, the fact that theresults from these regions will provide a significantly more definitiveresult in relation to the presence, or not, of hypermethylation thanwould be obtained if analysis was performed across the DNA region as awhole. This finding therefore both simplifies the screening process andincreases the sensitivity of large intestine neoplasia diagnosis.

The subregions which have been determined to exhibit particular utilityare listed below with reference to the gene and chromosomal regionwithin which they are found:

(1) BCAT1 subregions chr12:25101992-25102093 (SEQ ID NO:1 or thecorresponding minus strand) and chr12:25101909-25101995 (SEQ ID NO:2 orthe corresponding minus strand)

(2) IKZF1 subregions: chr7:50343867-50343961 (SEQ ID NO:3 or thecorresponding minus strand) and chr7:50343804-5033895 (SEQ ID NO:4 orthe corresponding minus strand)

(3) IRF4 subregions chr6:392036-392145 (SEQ ID NO:5 or the correspondingminus strand)

(4) GRASP subregions: chr12:52399672-52399922, chr12:52400821-52401051(SEQ ID NO:6 or the corresponding minus strand), chr12:52401407-52401664(SEQ ID NO:7 or the corresponding minus strand) chr12:52400866-52400973and Chr12:52401107-52401664.

(5) CAHM subregions: chr6:163834295-163834500 (SEQ ID NO:8),chr6:163834621-163834906, chr6:163834393-163834455 andchr6:163834393-163834519.

Without limiting the present invention to any one theory or mode ofaction, the skilled person may screen one or more subregions for eachgene marker.

Without limiting the present invention to any one theory or mode ofaction, DNA methylation is universal in bacteria, plants, and animals.DNA methylation is a type of chemical modification of DNA that is stableover rounds of cell division but does not involve changes in theunderlying DNA sequence of the organism. Chromatin and DNA modificationsare two important features of epigenetics and play a role in the processof cellular differentiation, allowing cells to stably maintain differentcharacteristics despite containing the same genomic material. Ineukaryotic organisms DNA methylation occurs only at the number 5 carbonof the cytosine pyrimidine ring. In mammals, DNA methylation occursmostly at the number 5 carbon of the cytosine of a CpG dinucleotide. CpGdinucleotides comprise approximately 1% human genome.

70-80% of all CpGs are methylated. CpGs may be grouped in clusterscalled “CpG islands” that are present in the 5′ regulatory regions ofmany genes and are frequently unmethylated. In many disease processessuch as cancer, gene promoters and/or CpG islands acquire abnormalhypermethylation, which is associated with heritable transcriptionalsilencing. DNA methylation may impact the transcription of genes in twoways. First, the methylation of DNA may itself physically impede thebinding of transcriptional proteins to the gene, thus blockingtranscription. Second, methylated DNA may be bound by proteins known asMethyl-CpG-binding domain proteins (MBDs). MBD proteins then recruitadditional proteins to the locus, such as histone deacetylases and otherchromatin remodelling proteins that can modify histones, thereby formingcompact, inactive chromatin termed silent chromatin. This link betweenDNA methylation and chromatin structure is very important. Inparticular, loss of Methyl-CpG-binding Protein 2 (MeCP2) has beenimplicated in Rett syndrome and Methyl-CpG binding domain protein 2(MBD2) mediates the transcriptional silencing of hypermethylated genesin cancer.

In humans, the process of DNA methylation is carried out by threeenzymes, DNA methyltransferase 1, 3a and 3b (DNMT1, DNMT3a, DNMT3b). Itis thought that DNMT3a and DNMT3b are the de novo methyltransferasesthat set up DNA methylation patterns early in development. DNMT1 is theproposed maintenance methyltransferase that is responsible for copyingDNA methylation patterns to the daughter strands during DNA replication.DNMT3L is a protein that is homologous to the other DNMT3s but has nocatalytic activity. Instead, DNMT3L assists the de novomethyltransferases by increasing their ability to bind to DNA andstimulating their activity. Finally, DNMT2 has been identified as an“enigmatic” DNA methylstransferase homolog, containing all 10 sequencemotifs common to all DNA methyltransferases; however, DNMT2 may notmethylate DNA but instead has been shown to methylate a small RNA.

“Methylation status” should therefore be understood as a reference tothe presence, absence and/or quantity of methylation at a particularnucleotide, or nucleotides, within a DNA region. The methylation statusof a particular DNA sequence (e.g. DNA region as described herein) canindicate the methylation state of every base in the sequence or canindicate the methylation state of a subset of the base pairs (e.g., ofcytosines or the methylation state of one or more specific restrictionenzyme recognition sequences) within the sequence, or can indicateinformation regarding regional methylation density within the sequencewithout providing precise information of where in the sequence themethylation occurs. The methylation status can optionally be representedor indicated by a “methylation value.” A methylation value can begenerated, for example, by quantifying the amount of intact DNA presentfollowing restriction digestion with a methylation dependent restrictionenzyme. In this example, if a particular sequence in the DNA isquantified using quantitative PCR, an amount of template DNAapproximately equal to a mock treated control indicates the sequence isnot highly methylated whereas an amount of template substantially lessthan occurs in the mock treated sample indicates the presence ofmethylated DNA at the sequence. Accordingly, a value, i.e., amethylation value, for example from the above described example,represents the methylation status and can thus be used as a quantitativeindicator of the methylation status. This is of particular use when itis desirable to compare the methylation status of a sequence in a sampleto a threshold value.

The term “methylation” shall be taken to mean the presence of a methylgroup added by the action of a DNA methyl transferase enzyme to acytosine base or bases in a region of nucleic acid, e.g. genomic DNA. Asdescribed herein, there are several methods known to those skilled inthe art for determining the level or degree of methylation of nucleicacid.

By “higher level” is meant that there are a higher number of methylatedCpG dinucleotides in the subject diagnosed than in a control sample,that is, either the proportion of DNA molecules methylated at aparticular CpG site is higher or there are a higher number of separateCpG sites methylated in the subject. It should be understood that theterms “enhanced” and “increased” are used interchangeably with the term“higher”.

The present invention is not to be limited by a precise number ofmethylated residues that are considered to be diagnostic of neoplasia ina subject, because some variation between patient samples will occur.The present invention is also not limited by positioning of themethylated residue.

Nevertheless, a number of specific cytosine residues which undergohypermethylation within these subregions have also been identified. Inanother embodiment, therefore, a screening method can be employed whichis specifically directed to assessing the methylation status of one ormore of either these residues or the corresponding cytosine at positionn+1 on the opposite DNA strand.

To this end, detailed in Table 2 are the cytosine residues which havebeen identified in this regard. It should be appreciated by the personof skill in the art that these individual residues are numbered byreference to Hg19, which also corresponds to the numbering of thespecific subregions listed hereinbefore and which can be furtheridentified when the coordinate numbering for each subregion is appliedto the corresponding subregion sequences which are provided in thesequence listing. It should be understood that these residues have beenidentified in the context of the subregion DNA. However, there are otherresidues which are hypermethylated outside the subregions themselves butwithin the larger DNA region from which the subregions derive.Accordingly, these specified residues represent a particularly usefulsubset of individual cytosine residues which undergo hypermethylationwithin the context of the DNA regions and subregions herein disclosed.These individual residues are grouped below according to the DNA regionwithin which they occur. These DNA regions are identified by referenceto both the Hg19 chromosomal coordinates and the gene region name.

To the extent that the method of the present invention includesanalysing the methylation of BCAT1, the subject residues:

chr12: 25101998 chr12: 25102003 chr12: 25102006 chr12: 25102009 chr12:25102017 chr12: 25102022 chr12: 25102039 chr12: 25102048 chr12: 25102050chr12: 25102053 chr12: 25102061 chr12: 25102063 chr12: 25102071 chrl12:25101921 chr12: 25101934 chr12: 25101943 chr12: 25101951 chr12: 25101962chr12: 25101964 chr12: 25101970or a corresponding cytosine at position n+1 on the opposite DNA strand.

To the extent that the method of the present invention includesanalysing the methylation of GRASP, the subject residues are:

chr12: 52399713 chr12: 52399731 chr12: 52399749 chr12: 52399783 chr12:52399796 chr12: 52399808 chr12: 52399823 chr12: 52399835 chr12: 52399891chr12: 52400847 chr12: 52400850 chr12: 52400859 chr12: 52400866 chr12:52400869 chr12: 52400873 chr12: 52400881 chr12: 52400886 chr12: 52400893chr12: 52400895 chr12: 52400899 chr12: 52400902 chr12: 52400907 chr12:52400913 chr12: 52400919 chr12: 52400932 chr12: 52400938 chr12: 52400958chr12: 52400962 chr12: 52400971 chr12: 52400973 chr12: 52400976 chr12:52400998 chr12: 52401008 chr12: 52401010 chr12: 52401012 chr12: 52401016chr12: 52401019 chr12: 52401025 chr12: 52401041 chr12: 52401044 chr12:52401053 chr12: 52401060 chr12: 52401064 chr12: 52401092 chr12: 52401118chr12: 52401438 chr12: 52401448 chr12: 52401460 chr12: 52401465 chr12:52401474 chr12: 52401477 chr12: 52401479 chr12: 52401483 chr12: 52401504chr12: 52401514 chr12: 52401523 chr12: 52401540 chr12: 52401553 chr12:52401576 chr12: 52401588 chr12: 52401595 chr12: 52401599 chr12: 52401604chr12: 52401606 chr12: 52401634 chr12: 52401640 chr12: 52401644 chr12:52401659 chr12: 52401160 chr12: 52401165 chr12: 52401174 chr12: 52401177chr12: 52401179 chr12: 52401183 chr12: 52401204 chr12: 52401215 chr12:52401223 chr12: 52401240 chr12: 52401253 chr12: 52401288 chr12: 52401295chr12: 52401299 chr12: 52401304 chr12: 52401334 chr12: 52401340 chr12:52401344 chr12: 52401359or a corresponding cytosine at position n+1 on the opposite DNA strand.

To the extent that the method of the present invention includesanalysing the methylation of CAHM, the subject residues are:

chr6: 163834330 chr6: 163834332 chr6: 163834357 chr6: 163834373 chr6:163834384 chr6: 163834390 chr6: 163834392 chr6: 163834406 chr6:163834412 chr6: 163834419 chr6: 163834443 chr6: 163834448 chr6:163834452 chr6: 163834464 chr6: 163834483 chr6: 163834653 chr6:163834660 chr6: 163834672 chr6: 163834675 chr6: 163834678 chr6:163834681 chr6: 163834815 chr6: 163834824 chr6: 163834835 chr6:163834840 chr6: 163834853 chr6: 163834855 chr6: 163834858 chr6:163834863 chr6: 163834869 chr6: 163834872or a corresponding cytosine at position n+1 on the opposite DNA strand.

To the extent that the method of the present invention includesanalysing the methylation of IKZF1, the subject residues are:

chr7: 50343869 chr7: 50343872 chr7: 50343883 chr7: 50343889 chr7:50343890 chr7: 50343897 chr7: 50343907 chr7: 50343909 chr7: 50343914chr7: 50343934 chr7: 50343939 chr7: 50343950 chr7: 50343959 chr7:50343805 chr7: 50343822 chr7: 50343824 chr7: 50343826 chr7: 50343829chr7: 50343831 chr7: 50343833 chr7: 50343838 chr7: 50343847 chr7:50343850 chr7: 50343858 chr7: 50343864 chr7: 50343869 chr7: 50343872chr7: 50343890or a corresponding cytosine at position n+1 on the opposite DNA strand.

To the extent that the method of the present invention includesanalysing the methylation of IRF4, the subject residues are:

chr6: 392036 chr6: 392047 chr6: 392049 chr6: 392057 chr6: 392060 chr6:392066 chr6: 392080 chr6: 392094 chr6: 392102 chr6: 392131or a corresponding cytosine at position n+1 on the opposite DNA strand.

The detection method of the present invention can be performed on anysuitable blood sample. To this end, reference to a “blood sample” shouldbe understood as a reference to any sample deriving from blood such as,but not limited to, whole blood, serum or plasma. The blood sample whichis tested according to the method of the present invention may be testeddirectly or may require some form of treatment prior to testing. Forexample, it may require permeabilisation prior to testing. In oneembodiment, the blood sample is a plasma sample.

To the extent that the DNA region of interest is present in a biologicalsample, the biological sample may be directly tested or else all or someof the nucleic acid present in the biological sample may be isolatedprior to testing. In yet another example, the sample may be partiallypurified or otherwise enriched prior to analysis. For example, to theextent that a biological sample comprises a very diverse cellpopulation, it may be desirable to enrich for a sub-population ofparticular interest. It is within the scope of the present invention forthe target cell population or molecules derived therefrom to be treatedprior to testing, for example, inactivation of live virus. It shouldalso be understood that the biological sample may be freshly harvestedor it may have been stored (for example by freezing) prior to testing orotherwise treated prior to testing (such as by undergoing culturing).

The choice of what type of sample is most suitable for testing inaccordance with the method disclosed herein will be dependent on thenature of the situation.

Although the present method is directed to classifying a large intestineneoplasm, the method of the invention is also useful as a means tomonitor disease progression. This can be important in situations such aswhere a decision has been made not to excise an early stage tumour or,even where surgery has been performed on the primary tumour, to monitorfor the development of metastases which may not have been visuallydetectable at the time that the primary tumor was identified. One mayalso seek to monitor a patient during a treatment regime for apremalignant or early stage malignancy in order to detect likelytransition to a higher stage malignancy.

The method of the invention can be used to evaluate individuals known orsuspected to have a neoplasia or as a routine clinical test, i.e., in anindividual not necessarily suspected to have a neoplasia.

Further, the present methods may be used to assess the efficacy of acourse of treatment. For example, the efficacy of an anti-cancertreatment can be assessed by monitoring DNA methylation of the sequencesdescribed herein over time in a mammal having cancer.

The method of the present invention is therefore useful as a one-timetest or as an on-going monitor of those individuals thought to be atrisk of neoplasia development or as a monitor of the effectiveness oftherapeutic or prophylactic treatment regimes directed to inhibiting orotherwise slowing neoplasia development. In these situations, mappingthe modulation of methylation levels in any one or more classes ofbiological samples is a valuable indicator of the status of anindividual or the effectiveness of a therapeutic or prophylactic regimewhich is currently in use.

Any method for detecting DNA methylation can be used in the methods ofthe present invention. A number of methods are available for detectionof differentially methylated DNA at specific loci in either primarytissue samples or in patient samples such as blood, urine, stool orsaliva (reviewed in Kristensen and Hansen Clin Chem. 55:1471-83, 2009;Ammerpohl et al. Biochim Biophys Acta. 1790:847-62, 2009; Shames et al.Cancer Lett. 251:187-98, 2007; Clark et al. Nat Protoc. 1:2353-64,2006). For analysis of the proportion or extent of DNA methylation in atarget gene, DNA is normally treated with sodium bisulfite and regionsof interest amplified using primers and PCR conditions that will amplifyindependently of the methylation status of the DNA. The methylation ofthe overall amplicon or individual CpG sites can then be assessed bysequencing, including pyrosequencing, restriction enzyme digestion(COBRA) or by melting curve analysis. Alternatively ligation-basedmethods for analysis of methylation at specific CpG sites may be used.Detection of aberrantly methylated DNA released from tumours and intobodily fluids is being developed as a means of cancer diagnosis. Here,in the case of hypermethylated sequences, it is necessary to usesensitive methods that allow the selective amplification of themethylated DNA sequence from a background of normal cellular DNA that isunmethylated. Such methods based on bisulfite-treated DNA, for example;include methylation selective PCR (MSP), Heavymethyl PCR, Headloop PCRand Helper-dependent chain reaction (PCT/AU2008/001475).

Briefly, in some embodiments, methods for detecting methylation includerandomly shearing or randomly fragmenting the genomic DNA, cutting theDNA with a methylation-dependent or methylation-sensitive restrictionenzyme and subsequently selectively identifying and/or analyzing the cutor uncut DNA. Selective identification can include, for example,separating cut and uncut DNA (e.g., by size) and quantifying a sequenceof interest that was cut or, alternatively, that was not cut. See, e.g.,U.S. Pat. No. 7,186,512. Alternatively, the method can encompassamplifying intact DNA after restriction enzyme digestion, thereby onlyamplifying DNA that was not cleaved by the restriction enzyme in thearea amplified. See, e.g., U.S. patent application Ser. Nos. 10/971,986;11/071,013; and Ser. No. 10/971,339. In some embodiments, amplificationcan be performed using primers that are gene specific. Alternatively,adaptors can be added to the ends of the randomly fragmented DNA, theDNA can be digested with a methylation-dependent ormethylation-sensitive restriction enzyme, intact DNA can be amplifiedusing primers that hybridize to the adaptor sequences. In this case, asecond step can be performed to determine the presence, absence orquantity of a particular gene in an amplified pool of DNA. In someembodiments, the DNA is amplified using real-time, quantitative PCR.

In some embodiments, the methods comprise quantifying the averagemethylation density in a target sequence within a population of genomicDNA. In some embodiments, the method comprises contacting genomic DNAwith a methylation-dependent restriction enzyme or methylation-sensitiverestriction enzyme under conditions that allow for at least some copiesof potential restriction enzyme cleavage sites in the locus to remainuncleaved; quantifying intact copies of the locus; and comparing thequantity of amplified product to a control value representing thequantity of methylation of control DNA, thereby quantifying the averagemethylation density in the locus compared to the methylation density ofthe control DNA.

The quantity of methylation of a locus of DNA can be determined byproviding a sample of genomic DNA comprising the locus, cleaving the DNAwith a restriction enzyme that is either methylation-sensitive ormethylation-dependent, and then quantifying the amount of intact DNA orquantifying the amount of cut DNA at the DNA locus of interest. Theamount of intact or cut DNA will depend on the initial amount of genomicDNA containing the locus, the amount of methylation in the locus, andthe number (i.e., the fraction) of nucleotides in the locus that aremethylated in the genomic DNA. The amount of methylation in a DNA locuscan be determined by comparing the quantity of intact DNA or cut DNA toa control value representing the quantity of intact DNA or cut DNA in asimilarly-treated DNA sample. The control value can represent a known orpredicted number of methylated nucleotides. Alternatively, the controlvalue can represent the quantity of intact or cut DNA from the samelocus in another (e.g., normal, non-diseased) cell or a second locus.

By using at least one methylation-sensitive or methylation-dependentrestriction enzyme under conditions that allow for at least some copiesof potential restriction enzyme cleavage sites in the locus to remainuncleaved and subsequently quantifying the remaining intact copies andcomparing the quantity to a control, average methylation density of alocus can be determined. A methylation-sensitive enzyme is one whichcuts DNA if its recognition sequence is unmethylated while amethylation-dependent enzyme cuts DNA if its recognition sequence ismethylated. If the methylation-sensitive restriction enzyme is contactedto copies of a DNA locus under conditions that allow for at least somecopies of potential restriction enzyme cleavage sites in the locus toremain uncleaved, then the remaining intact DNA will be directlyproportional to the methylation density, and thus may be compared to acontrol to determine the relative methylation density of the locus inthe sample. Similarly, if a methylation-dependent restriction enzyme iscontacted to copies of a DNA locus under conditions that allow for atleast some copies of potential restriction enzyme cleavage sites in thelocus to remain uncleaved, then the remaining intact DNA will beinversely proportional to the methylation density, and thus may becompared to a control to determine the relative methylation density ofthe locus in the sample. Such assays are disclosed in, e.g., U.S. patentapplication Ser. No. 10/971,986.

Kits for the above methods can include, e.g., one or more ofmethylation-dependent restriction enzymes, methylation-sensitiverestriction enzymes, amplification (e.g., PCR) reagents, probes and/orprimers.

Quantitative amplification methods (e.g., quantitative PCR orquantitative linear amplification) can be used to quantify the amount ofintact DNA within a locus flanked by amplification primers followingrestriction digestion. Methods of quantitative amplification aredisclosed in, e.g., U.S. Pat. Nos. 6,180,349; 6,033,854; and 5,972,602,as well as in, e.g., Gibson et al., Genome Research 6:995-1001 (1996);DeGraves, et al., Biotechniques 34(1):106-10, 112-5 (2003); Deiman B, etal., Mol. Biotechnol. 20(2):163-79 (2002). Amplifications may bemonitored in “real time.”

Additional methods for detecting DNA methylation can involve genomicsequencing before and after treatment of the DNA with bisulfite. See,e.g., Frommer et al., Proc. Natl. Acad. Sci. USA 89:1827-1831 (1992).When sodium bisulfite is contacted to DNA, unmethylated cytosine isconverted to uracil, while methylated cytosine is not modified.

In some embodiments, restriction enzyme digestion of PCR productsamplified from bisulfite-converted DNA is used to detect DNAmethylation. See, e.g., Sadri & Hornsby, Nucl. Acids Res. 24:5058-5059(1996); Xiong & Laird, Nucleic Acids Res. 25:2532-2534 (1997).

In some embodiments, a methylation-specific PCR (“MSP”) reaction is usedalone or in combination with other methods to detect DNA methylation. AnMSP assay entails initial modification of DNA by sodium bisulfite,converting all unmethylated, but not methylated, cytosines to uracil,and subsequent amplification with primers specific for methylated versesunmethylated DNA. See, Herman et al. Proc. Natl. Acad. Sci. USA93:9821-9826 (1996); U.S. Pat. No. 5,786,146.

In some embodiments, a MethyLight assay is used alone or in combinationwith other methods to detect DNA methylation (see, Eads et al., CancerRes. 59:2302-2306 (1999)). Briefly, in the MethyLight process genomicDNA is converted in a sodium bisulfite reaction (the bisulfite processconverts unmethylated cytosine residues to uracil). Amplification of aDNA sequence of interest is then performed using PCR primers thathybridize to CpG dinucleotides. By using primers that hybridize only tosequences resulting from bisulfite conversion of methylated DNA, (oralternatively to unmethylated sequences) amplification can indicatemethylation status of sequences where the primers hybridize.Furthermore, the amplification product can be detected with a probe thatspecifically binds to a sequence resulting from bisulfite treatment ofan unmethylated DNA. If desired, both primers and probes can be used todetect methylation status. Thus, kits for use with MethyLight caninclude sodium bisulfite as well as primers or detectably-labelledprobes (including but not limited to Taqman or molecular beacon probes)that distinguish between methylated and unmethylated DNA that have beentreated with bisulfite. Other kit components can include, e.g., reagentsnecessary for amplification of DNA including but not limited to, PCRbuffers, deoxynucleotides; and a thermostable polymerase.

In some embodiments, a Ms-SNuPE (Methylation-sensitive Single NucleotidePrimer Extension) reaction is used alone or in combination with othermethods to detect DNA methylation (see, Gonzalgo & Jones, Nucleic AcidsRes. 25:2529-2531 (1997)). The Ms-SNuPE technique is a quantitativemethod for assessing methylation differences at specific CpG sites basedon bisulfite treatment of DNA, followed by single-nucleotide primerextension (Gonzalgo & Jones, supra). Briefly, genomic DNA is reactedwith sodium bisulfite to convert unmethylated cytosine to uracil whileleaving 5-methylcytosine unchanged. Amplification of the desired targetsequence is then performed using PCR primers specific forbisulfite-converted DNA, and the resulting product is isolated and usedas a template for methylation analysis at the CpG site(s) of interest.

Typical reagents (e.g., as might be found in a typical Ms-SNuPE-basedkit) for Ms-SNuPE analysis can include, but are not limited to: PCRprimers for specific gene (or methylation-altered DNA sequence or CpGisland); optimized PCR buffers and deoxynucleotides; gel extraction kit;positive control primers; Ms-SNuPE primers for a specific gene; reactionbuffer (for the Ms-SNuPE reaction); and detectably-labelled nucleotides.Additionally, bisulfite conversion reagents may include: DNAdenaturation buffer; sulfonation buffer; DNA recovery regents or kit(e.g., precipitation, ultrafiltration, affinity column); desulfonationbuffer; and DNA recovery components.

Additional methylation detection methods include, but are not limitedto, methylated CpG island amplification (see, Toyota et al., Cancer Res.59:2307-12 (1999)) and those described in, e.g., U.S. Patent Publication2005/0069879; Rein, et al. Nucleic Acids Res. 26 (10): 2255-64 (1998);Olek, et al. Nat. Genet. 17(3): 275-6 (1997); and PCT Publication No. WO00/70090.

More detailed information in relation to several of these generallydescribed methods is provided below:

(a) Probe or Primer Design and/or Production

Several methods described herein for the diagnosis of a neoplasia useone or more probes and/or primers. Methods for designing probes and/orprimers for use in, for example, PCR or hybridization are known in theart and described, for example, in Dieffenbach and Dveksler (Eds) (In:PCR Primer: A Laboratory Manual, Cold Spring Harbor Laboratories, N Y,1995). Furthermore, several software packages are publicly availablethat design optimal probes and/or primers for a variety of assays, e.g.Primer 3 available from the Center for Genome Research, Cambridge,Mass., USA.

Clearly, the potential use of the probe or primer should be consideredduring its design. For example, should the probe or primer be producedfor use in a methylation specific PCR or ligase chain reaction (LCR)assay the nucleotide at the 3′ end (or 5′ end in the case of LCR) shouldpreferably correspond to a methylated nucleotide in a nucleic acid.

Probes and/or primers useful for detection of a sequence associated witha neoplasia are assessed, for example, to determine those that do notform hairpins, self-prime or form primer dimers (e.g. with another probeor primer used in a detection assay). Furthermore, a probe or primer (orthe sequence thereof) is often assessed to determine the temperature atwhich it denatures from a target nucleic acid (i.e. the meltingtemperature of the probe or primer, or Tm). Methods for estimating Tmare known in the art and described, for example, in Santa Lucia, Proc.Natl. Acad. Sci. USA, 95: 1460-1465, 1995 or Bresslauer et al., Proc.Natl. Acad. Sci. USA, 83: 3746-3750, 1986.

Methods for producing/synthesizing a probe or primer of the presentinvention are known in the art. For example, oligonucleotide synthesisis described, in Gait (Ed) (In: Oligonucleotide Synthesis: A PracticalApproach, IRL Press, Oxford, 1984). For example, a probe or primer maybe obtained by biological synthesis (e.g. by digestion of a nucleic acidwith a restriction endonuclease) or by chemical synthesis. For shortsequences (up to about 100 nucleotides) chemical synthesis ispreferable.

For longer sequences standard replication methods employed in molecularbiology are useful, such as, for example, the use of M13 for singlestranded DNA as described by Messing, Methods Enzymol, 101, 20-78, 1983.Other methods for oligonucleotide synthesis include, for example,phosphotriester and phosphodiester methods (Narang, et al. Meth. Enzymol68: 90, 1979) and synthesis on a support (Beaucage, et al. TetrahedronLetters 22:1859-1862, 1981) as well as phosphoramidate technique,Caruthers, M. H., et al., Methods in Enzymology, Vol. 154, pp. 287-314(1988), and others described in “Synthesis and Applications of DNA andRNA,” S. A. Narang, editor, Academic Press, New York, 1987, and thereferences cited therein. Probes comprising locked nucleic acid (LNA)are synthesized as described, for example, in Nielsen et al. J. Chem.Soc. Perkin Trans., 1:3423, 1997; Singh and Wengel, Chem. Commun. 1247,1998. While, probes comprising peptide-nucleic acid (PNA) aresynthesized as described, for example, in Egholm et al., Am. Chem. Soc.,114:1895, 1992; Egholm et al., Nature, 365:566, 1993; and Orum et al.,Nucl. Acids Res., 21:5332, 1993.

(b) Methylation-Sensitive Endonuclease Digestion of DNA

In one example, the increased methylation in a sample is determinedusing a process comprising treating the nucleic acid with an amount of amethylation-sensitive restriction endonuclease enzyme under conditionssufficient for nucleic acid to be digested and then detecting thefragments produced. Exemplary methylation-sensitive endonucleasesinclude, for example, HhaI or HpaII. Preferably, assays include internalcontrols that are digested with a methylation-insensitive enzyme havingthe same specificity as the methylation-sensitive enzyme employed. Forexample, the methylation-insensitive enzyme MspI is an isoschizomer ofthe methylation-sensitive enzyme HpaII.

Hybridization Assay Formats

In one example, the digestion of nucleic acid is detected by selectivehybridization of a probe or primer to the undigested nucleic acid.Alternatively, the probe selectively hybridizes to both digested andundigested nucleic acid but facilitates differentiation between bothforms, e.g., by electrophoresis. Suitable detection methods forachieving selective hybridization to a hybridization probe include, forexample, Southern or other nucleic acid hybridization (Kawai et al.,Mol. Cell. Biol. 14:7421-7427, 1994; Gonzalgo et al., Cancer Res.57:594-599, 1997).

Suitable hybridization conditions are determined based on the meltingtemperature (Tm) of a nucleic acid duplex comprising the probe. Theskilled artisan will be aware that optimum hybridization reactionconditions should be determined empirically for each probe, althoughsome generalities can be applied. Preferably, hybridizations employingshort oligonucleotide probes are performed at low to medium stringency.In the case of a GC rich probe or primer or a longer probe or primer ahigh stringency hybridization and/or wash is preferred. A highstringency is defined herein as being a hybridization and/or washcarried out in about 0.1×SSC buffer and/or about 0.1% (w/v) SDS, orlower salt concentration, and/or at a temperature of at least 65° C., orequivalent conditions. Reference herein to a particular level ofstringency encompasses equivalent conditions using wash/hybridizationsolutions other than SSC known to those skilled in the art.

In accordance with the present example, a difference in the fragmentsproduced for the test sample and a negative control sample is indicativeof the subject having a neoplasia. Similarly, in cases where the controlsample comprises data from a tumor, cancer tissue or a cancerous cell orpre-cancerous cell, similarity, albeit not necessarily absoluteidentity, between the test sample and the control sample is indicativeof a positive diagnosis (i.e. cancer).

Amplification Assay Formats

In an alternative example, the fragments produced by the restrictionenzyme are detected using an amplification system, such as, for example,polymerase chain reaction (PCR), rolling circle amplification (RCA),inverse polymerase chain reaction (iPCR), in situ PCR (Singer-Sam etal., Nucl. Acids Res. 18:687, 1990), strand displacement amplification(SDA) or cycling probe technology.

Methods of PCR are known in the art and described, for example, byMcPherson et al., PCR: A Practical Approach. (series eds, D. Rickwoodand B. D. Hames), IRL Press Limited, Oxford. pp 1-253, 1991 and byDieffenbach (ed) and Dveksler (ed) (In: PCR Primer: A Laboratory Manual,Cold Spring Harbour Laboratories, N Y, 1995), the contents of which areeach incorporated in their entirety by way of reference. Generally, forPCR two non-complementary nucleic acid primer molecules comprising atleast about 18 nucleotides in length, and more preferably at least 20-30nucleotides in length are hybridized to different strands of a nucleicacid template molecule at their respective annealing sites, and specificnucleic acid molecule copies of the template that intervene theannealing sites are amplified enzymatically. Amplification products maybe detected, for example, using electrophoresis and detection with adetectable marker that binds nucleic acids. Alternatively, one or moreof the oligonucleotides are labelled with a detectable marker (e.g. afluorophore) and the amplification product detected using, for example,a lightcycler (Perkin Elmer, Wellesley, Mass., USA, Roche AppliedScience, Indianapolis, Ind., USA).

Strand displacement amplification (SDA) utilizes oligonucleotideprimers, a DNA polymerase and a restriction endonuclease to amplify atarget sequence. The oligonucleotides are hybridized to a target nucleicacid and the polymerase is used to produce a copy of the regionintervening the primer annealing sites. The duplexes of copied nucleicacid and target nucleic acid are then nicked with an endonuclease thatspecifically recognizes a sequence at the beginning of the copiednucleic acid. The DNA polymerase recognizes the nicked DNA and producesanother copy of the target region at the same time displacing thepreviously generated nucleic acid. The advantage of SDA is that itoccurs in an isothermal format, thereby facilitating high-throughputautomated analysis.

Cycling Probe Technology uses a chimeric synthetic primer that comprisesDNA-RNA-DNA that is capable of hybridizing to a target sequence. Uponhybridization to a target sequence the RNA-DNA duplex formed is a targetfor RNaseH thereby cleaving the primer. The cleaved primer is thendetected, for example, using mass spectrometry or electrophoresis.

For primers that flank or are adjacent to a methylation-sensitiveendonuclease recognition site, it is preferred that such primers flankonly those sites that are hypermethylated in neoplasia to ensure that adiagnostic amplification product is produced. In this regard, anamplification product will only be produced when the restriction site isnot cleaved, i.e., when it is methylated. Accordingly, detection of anamplification product indicates that the CpG dinucleotide/s of interestis/are methylated.

As will be known to the skilled artisan, the precise length of theamplified product will vary depending upon the distance between theprimers. Clearly this form of analysis may be used to determine themethylation status of a plurality of CpG dinucleotides provided thateach dinucleotide is within a methylation sensitive restrictionendonuclease site. In these methods, one or more of the primers may belabelled with a detectable marker to facilitate rapid detection ofamplified nucleic acid, for example, a fluorescent label (e.g. Cy5 orCy3) or a radioisotope (e.g. ³²P).

The amplified nucleic acids are generally analyzed using, for example,non-denaturing agarose gel electrophoresis, non-denaturingpolyacrylamide gel electrophoresis, mass spectrometry, liquidchromatography (e.g. HPLC or dHPLC), or capillary electrophoresis. (e.g.MALDI-TOF). High throughput detection methods, such as, for example,matrix-assisted laser desorption/ionization time of flight (MALDI-TOF),electrospray ionization (ESI), mass spectrometry (including tandem massspectrometry, e.g. LC MS/MS), biosensor technology, evanescentfiber-optics technology or DNA chip technology (e.g., WO98/49557; WO96/17958; Fodor et al., Science 767-773, 1991; U.S. Pat. Nos. 5,143,854;and 5,837,832, the contents of which are all incorporated herein byreference), are especially preferred for all assay formats describedherein. Alternatively, amplification of a nucleic acid may becontinuously monitored using a melting curve analysis method asdescribed herein and/or in, for example, U.S. Pat. No. 6,174,670, whichis incorporated herein by reference.

(c) Other Assay Formats

In an alternative example, the increased methylation in a sample isdetermined by performing a process comprising treating chromatincontaining the nucleic acid with an amount of DNaseI under conditionssufficient for nucleic acid to be digested and then detecting thefragments produced. This assay format is predicated on the understandingthat chromatin containing methylated DNA, e.g., hyper methylated DNA,has a more tightly-closed conformation than non-hyper methylated DNAand, as a consequence, is less susceptible to endonuclease digestion byDNase I.

In accordance with this method, DNA fragments of different lengths areproduced by DNase I digestion of methylated compared to non-methylatedDNA. Such different DNA fragments are detected, for example, using anassay described earlier. Alternatively, the DNA fragments are detectedusing PCR-SSCP essentially as described, for example, in Gregory andFeil, Nucleic Acids Res., 27, e32i-e32iv, 1999. In adapting PCR-SSCP tothe present invention, amplification primers flanking or comprising oneor more CpG dinucleotides in a nucleic acid that are resistant to DNaseI digestion in a neoplasia sample but not resistant to DNase I digestionin a healthy/normal control or healthy/normal test sample are used toamplify the DNase I-generated fragments. In this case, the production ofa specific nucleic acid fragment using DNase I is diagnostic ofneoplasia, because the DNA is not efficiently degraded. In contrast,template DNA from a healthy/normal subject sample is degraded by theaction of DNase I and, as a consequence, amplification fails to producea discrete amplification product. Alternative methods to PCR-SSCP, suchas for example, PCR-dHPLC are also known in the art and contemplated bythe present invention.

(d) Selective Mutagenesis of Non-Methylated DNA

In an alternative method the increased methylation in a sample isdetermined using a process comprising treating the nucleic acid with anamount of a compound that selectively mutates a non-methylated cytosineresidue within a CpG dinucleotide under conditions sufficient to inducemutagenesis.

Preferred compounds mutate cytosine to uracil or thymidine, such as, forexample, a salt of bisulfite, e.g., sodium bisulfite or potassiumbisulfite (Frommer et al., 1992, supra). Bisulfite treatment of DNA isknown to distinguish methylated from non-methylated cytosine residues,by mutating cytosine residues that are not protected by methylation,including cytosine residues that are not within a CpG dinucleotide orthat are positioned within a CpG dinucleotide that is not subject tomethylation.

Sequence Based Detection

In one example, the presence of one or more mutated nucleotides or thenumber of mutated sequences is determined by sequencing mutated DNA. Oneform of analysis comprises amplifying mutated nucleic acid using anamplification reaction described herein, for example, PCR. The amplifiedproduct is then directly sequenced or cloned and the cloned productsequenced. Methods for sequencing DNA are known in the art and includefor example, the dideoxy chain termination method or the Maxam-Gilbertmethod (see Sambrook et al., Molecular Cloning, A Laboratory Manual (2ndEd., CSHP, New York 1989) or Zyskind et al., Recombinant DNA LaboratoryManual, (Acad. Press, 1988)).

As the treatment of nucleic acid with a compound, such as, for example,bisulfite results in non-methylated cytosines being mutated to uracil(and hence thymidine after an amplification process), analysis of thesequence determines the presence or absence of a methylated nucleotide.For example, by comparing the sequence obtained using a control sampleor a sample that has not been treated with bisulfite, or the knownnucleotide sequence of the region of interest with a treated samplefacilitates the detection of differences in the nucleotide sequence. Anythymine residue detected at the site of a cytosine in the treated samplecompared to a control or untreated sample may be considered to be causedby mutation as a result of bisulfite treatment. Suitable methods for thedetection of methylation using sequencing of bisulfite treated nucleicacid are described, for example, in Frommer et al., 1992, supra or Clarket al., Nucl. Acids Res. 22:2990-2997, 1994.

In another method, the presence of a mutated or non-mutated nucleotidein a bisulfite treated sample is detected using pyrosequencing, such as,for example, as described in Uhlmann et al., Electrophoresis, 23:4072-4079, 2002. Essentially this method is a form of real-timesequencing that uses a primer that hybridizes to a site adjacent orclose to the site of a cytosine that is methylated. Followinghybridization of the primer and template in the presence of a DNApolymerase each of four modified deoxynucleotide triphosphates are addedseparately according to a predetermined dispensation order. Only anadded nucleotide that is complementary to the bisulfite treated sampleis incorporated and inorganic pyrophosphate (PPi) is liberated. The PPithen drives a reaction resulting in production of detectable levels oflight. Such a method allows determination of the identity of a specificnucleotide adjacent to the site of hybridization of the primer.

Methods of solid phase pyrosequencing are known in the art and reviewedin, for example, Landegren et al., Genome Res., 8(8): 769-776, 1998.Such methods enable the high-throughput detection of methylation of anumber of CpG dinucleotides.

A related method for determining the sequence of a bisulfite treatednucleotide is methylation-sensitive single nucleotide primer extension(Me-SnuPE) or SNaPmeth. Suitable methods are described, for example, inGonzalgo and Jones, 1997, supra, or Uhlmann et al., Electrophoresis,23:4072-4079, 2002. An oligonucleotide is used that hybridizes to theregion of a nucleic acid adjacent to the site of a cytosine that ismethylated. This oligonucleotide is then used in a primer extensionprotocol with a polymerase and a free nucleotide diphosphate ordideoxynucleotide triphosphate that corresponds to either or any of thepossible bases that occur at this site following bisulfite treatment(i.e., thymine or cytosine). Preferably, the nucleotide-diphosphate islabelled with a detectable marker (e.g. a fluorophore). Following primerextension, unbound labelled nucleotide diphosphates are removed, e.g.using size exclusion chromatography or electrophoresis, or hydrolyzed,using for example, alkaline phosphatase, and the incorporation of thelabelled nucleotide to the oligonucleotide is detected, indicating thebase that is present at the site.

Clearly other high throughput sequencing methods are encompassed by thepresent invention. Such methods include, for example, solid phaseminisequencing (as described, for example, in Southern et al., Genomics,13:1008-1017, 1992), or minisequencing with FRET (as described, forexample, in Chen and Kwok, Nucleic Acids Res. 25:347-353, 1997).

Restriction Endonuclease-Based Assay Format

In one method, the presence of a non-mutated sequence is detected usingcombined bisulfite restriction analysis (COBRA) essentially as describedin Xiong and Laird, 2001, supra. This method exploits the differences inrestriction enzyme recognition sites between methylated and unmethylatednucleic acid after treatment with a compound that selectively mutates anon-methylated cytosine residue, e.g., bisulfite.

Following bisulfite treatment a region of interest comprising one ormore CpG dinucleotides that are methylated and are included in arestriction endonuclease recognition sequence is amplified using anamplification reaction described herein, e.g., PCR. The amplifiedproduct is then contacted with the restriction enzyme that cleaves atthe site of the CpG dinucleotide for a time and under conditionssufficient for cleavage to occur. A restriction site may be selected toindicate the presence or absence of methylation. For example, therestriction endonuclease TaqI cleaves the sequence TCGA, followingbisulfite treatment of a non-methylated nucleic acid the sequence willbe TTGA and, as a consequence, will not be cleaved. The digested and/ornon-digested nucleic acid is then detected using a detection means knownin the art, such as, for example, electrophoresis and/or massspectrometry. The cleavage or non-cleavage of the nucleic acid isindicative of cancer in a subject. Clearly, this method may be employedin either a positive read-out or negative read-out system for thediagnosis of a cancer.

Positive Read-Out Assay Format

In one embodiment, the assay format of the invention comprises apositive read-out system in which DNA from a sample that has beentreated, for example, with bisulfite is detected as a positive signal.Preferably, the non-hypermethylated DNA from a healthy or normal controlsubject is not detected or only weakly detected.

In a preferred embodiment, the increased methylation in a subject sampleis determined using a process comprising:

(i) treating the nucleic acid with an amount of a compound thatselectively mutates a non-methylated cytosine residue under conditionssufficient to induce mutagenesis thereby producing a mutated nucleicacid;

(ii) hybridizing a nucleic acid to a probe or primer comprising anucleotide sequence that is complementary to a sequence comprising amethylated cytosine residue under conditions such that selectivehybridization to the non-mutated nucleic acid occurs; and

(iii) detecting the selective hybridization.

In this context, the term “selective hybridization” means thathybridization of a probe or primer to the non-mutated nucleic acidoccurs at a higher frequency or rate, or has a higher maximum reactionvelocity, than hybridization of the same probe or primer to thecorresponding mutated sequence. Preferably, the probe or primer does nothybridize to the non-methylated sequence carrying the mutation(s) underthe reaction conditions used.

Hybridization-Based Assay Format

In one embodiment, the hybridization is detected using Southern, dotblot, slot blot or other nucleic acid hybridization means (Kawai et al.,1994, supra; Gonzalgo et al., 1997, supra). Subject to appropriate probeselection, such assay formats are generally described herein above andapply mutatis mutandis to the presently described selective mutagenesisapproach.

Preferably, a ligase chain reaction format is employed to distinguishbetween a mutated and non-mutated nucleic acid. Ligase chain reaction(described in EP 320,308 and U.S. Pat. No. 4,883,750) uses at least twooligonucleotide probes that anneal to a target nucleic acid in such away that they are juxtaposed on the target nucleic acid. In a ligasechain reaction assay, the target nucleic acid is hybridized to a firstprobe that is complementary to a diagnostic portion of the targetsequence (the diagnostic probe) e.g., a nucleic acid comprising one ormore methylated CpG dinucleotide(s), and with a second probe that iscomplementary to a nucleotide sequence contiguous with the diagnosticportion (the contiguous probe), under conditions wherein the diagnosticprobe remains bound substantially only to the target nucleic acid. Thediagnostic and contiguous probes can be of different lengths and/or havedifferent melting temperatures such that the stringency of thehybridization can be adjusted to permit their selective hybridization tothe target, wherein the probe having the higher melting temperature ishybridized at higher stringency and, following washing to remove unboundand/or non-selectively bound probe, the other probe having the lowermelting temperature is hybridized at lower stringency. The diagnosticprobe and contiguous probe are then covalently ligated such as, forexample, using T4 DNA ligase, to thereby produce a larger target probethat is complementary to the target sequence, and the probes that arenot ligated are removed by modifying the hybridization stringency. Inthis respect, probes that have not been ligated will selectivelyhybridize under lower stringency hybridization conditions than probesthat have been ligated. Accordingly, the stringency of the hybridizationcan be increased to a stringency that is at least as high as thestringency used to hybridize the longer probe, and preferably at ahigher stringency due to the increased length contributed by the shorterprobe following ligation.

In another example, one or both of the probes is labelled such that thepresence or absence of the target sequence can be tested by melting thetarget-probe duplex, eluting the dissociated probe, and testing for thelabel(s). Where both probes are labelled, different ligands are used topermit distinction between the ligated and unligated probes, in whichcase the presence of both labels in the same eluate fraction confirmsthe ligation event. If the target nucleic acid is bound to a solidmatrix e.g., in a Southern hybridization, slot blot, dot blot, ormicrochip assay format, the presence of both the diagnostic andcontiguous probes can be determined directly.

Methylation specific microarrays (MSO) are also useful fordifferentiating between a mutated and non-mutated sequence. A suitablemethod is described, for example, in Adorjan et al. Nucl. Acids Res.,30: e21, 2002. MSO uses nucleic acid that has been treated with acompound that selectively mutates a non-methylated cytosine residue(e.g., bisulfite) as template for an amplification reaction thatamplifies both mutant and non-mutated nucleic acid. The amplification isperformed with at least one primer that comprises a detectable label,such as, for example, a fluorophore, e.g., Cy3 or Cy5.

To produce a microarray for detection of mutated nucleic acidoligonucleotides are spotted onto, for example, a glass slide,preferably, with a degree of redundancy (for example, as described inGolub et al., Science, 286:531-537, 1999). Preferably, for each CpGdinucleotide analyzed two different oligonucleotides are used. Eacholigonucleotide comprises a sequence N₂-16CGN₂₋₁₆ or N₂-16TGN₂-16(wherein N is a number of nucleotides adjacent or juxtaposed to the CpGdinucleotide of interest) reflecting the methylated or non-methylatedstatus of the CpG dinucleotides.

The labelled amplification products are then hybridized to theoligonucleotides on the microarray under conditions that enabledetection of single nucleotide differences. Following washing to removeunbound amplification product, hybridization is detected using, forexample, a microarray scanner. Not only does this method allow fordetermination of the methylation status of a large number of CpGdinucleotides, it is also semi-quantitative, enabling determination ofthe degree of methylation at each CpG dinucleotide analyzed. As theremay be some degree of heterogeneity of methylation in a single sample,such quantification may assist in the diagnosis of cancer.

Amplification-Based Assay Format

In an alternative example, the hybridization is detected using anamplification system. In methylation-specific PCR formats (MSP; Hermanet al. Proc. Natl. Acad. Sci. USA 93:9821-9826, 1992), the hybridizationis detected using a process comprising amplifying the bisulfite-treatedDNA. Accordingly, by using one or more probe or primer that annealsspecifically to the unmutated sequence under moderate and/or highstringency conditions an amplification product is only produced using asample comprising a methylated nucleotide. Alternate assays that providefor selective amplification of either the methylated or the unmethylatedcomponent from a mixture of bisulfite-treated DNA are provided byCottrell et al., Nucl. Acids Res. 32: e10, 2003 (HeavyMethyl PCR), Randet al. Nucl. Acids Res. 33:e127, 2005 (Headloop PCR), Rand et al.Epigenetics 1:94-100, 2006 (Bisulfite Differential Denaturation PCR) andPCT/AU07/000389 (End-specific PCR).

Any amplification assay format described herein can be used, such as,for example, polymerase chain reaction (PCR), rolling circleamplification (RCA), inverse polymerase chain reaction (iPCR), in situPCR (Singer-Sam et al., 1990, supra), strand displacement amplification,or cycling probe technology. PCR techniques have been developed fordetection of gene mutations (Kuppuswamy et al., Proc. Natl. Acad. Sci.USA 88:1143-1147, 1991) and quantitation of allelic-specific expression(Szabo and Mann, Genes Dev. 9: 3097-3108, 1995; and Singer-Sam et al.,PCR Methods Appl. 1: 160-163, 1992). Such techniques use internalprimers, which anneal to a PCR-generated template and terminateimmediately 5′ of the single nucleotide to be assayed. Such as format isreadily combined with ligase chain reaction as described herein above.The use of a real-time quantitative assay format is also useful. Subjectto the selection of appropriate primers, such assay formats aregenerally described herein above and apply mutatis mutandis to thepresently described selective mutagenesis approach.

Methylation-specific melting-curve analysis (essentially as described inWorm et al., Clin. Chem., 47:1183-1189, 2001) is also contemplated bythe present invention. This process exploits the difference in meltingtemperature in amplification products produced using bisulfite treatedmethylated or unmethylated nucleic acid. In essence, non-discriminatoryamplification of a bisulfite treated sample is performed in the presenceof a fluorescent dye that specifically binds to double stranded DNA(e.g., SYBR Green I). By increasing the temperature of the amplificationproduct while monitoring fluorescence the melting properties and thusthe sequence of the amplification product is determined. A decrease inthe fluorescence reflects melting of at least a domain in theamplification product. The temperature at which the fluorescencedecreases is indicative of the nucleotide sequence of the amplifiednucleic acid, thereby permitting the nucleotide at the site of one ormore CpG dinucleotides to be determined. As the sequence of the nucleicacids amplified using the present invention.

The present invention also encompasses the use of real-time quantitativeforms of PCR, such as, for example, TaqMan (Holland et al., Proc. Natl.Acad. Sci. USA, 88:7276-7280, 1991; Lee et al., Nucleic Acid Res.21:3761-3766, 1993) to perform this embodiment. For example, theMethylLight method of Eads et al., Nucl. Acids Res. 28: E32, 2000 uses amodified TaqMan assay to detect methylation of a CpG dinucleotide.Essentially, this method comprises treating a nucleic acid sample withbisulfite and amplifying nucleic acid comprising one or more CpGdinucleotides that are methylated in a neoplastic cell and not in acontrol sample using an amplification reaction, e.g., PCR. Theamplification reaction is performed in the presence of threeoligonucleotides, a forward and reverse primer that flank the region ofinterest and a probe that hybridizes between the two primers to the siteof the one or more methylated CpG dinucleotides. The probe is duallabelled with a 5′ fluorescent reporter and a 3′ quencher (or viceversa). When the probe is intact, the quencher dye absorbs thefluorescence of the reporter due to their proximity. Following annealingof to the PCR product the probe is cleaved by 5′ to 3′ exonucleaseactivity of, for example, Taq DNA polymerase. This cleavage releases thereporter from the quencher thereby resulting in an increasedfluorescence signal that can be used to estimate the initial templatemethylation level. By using a probe or primer that selectivelyhybridizes to unmutated nucleic acid (i.e. methylated nucleic acid) thelevel of methylation is determined, e.g., using a standard curve.

Alternatively, rather than using a labelled probe that requirescleavage, a probe, such as, for example, a Molecular Beacon is used(see, for example, Mhlanga and Malmberg, Methods 25:463-471, 2001).Molecular beacons are single stranded nucleic acid molecules with astem-and-loop structure. The loop structure is complementary to theregion surrounding the one or more CpG dinucleotides that are methylatedin a neoplastic sample and not in a control sample. The stem structureis formed by annealing two “arms” complementary to each other, which areon either side of the probe (loop). A fluorescent moiety is bound to onearm and a quenching moiety that suppresses any detectable fluorescencewhen the molecular beacon is not bound to a target sequence is bound tothe other arm. Upon binding of the loop region to its target nucleicacid the arms are separated and fluorescence is detectable. However,even a single base mismatch significantly alters the level offluorescence detected in a sample. Accordingly, the presence or absenceof a particular base is determined by the level of fluorescencedetected. Such an assay facilitates detection of one or more unmutatedsites (i.e. methylated nucleotides) in a nucleic acid.

Fluorescently labelled locked nucleic acid (LNA) molecules orfluorescently labelled protein-nucleic acid (PNA) molecules are usefulfor the detection of nucleotide differences (e.g., as described inSimeonov and Nikiforov, Nucleic Acids Research, 30(17):1-5, 2002). LNAand PNA molecules bind, with high affinity, to nucleic acid, inparticular, DNA. Fluorophores (in particular, rhodomine orhexachlorofluorescein) conjugated to the LNA or PNA probe fluoresce at asignificantly greater level upon hybridization of the probe to targetnucleic acid. However, the level of increase of fluorescence is notenhanced to the same level when even a single nucleotide mismatchoccurs. Accordingly, the degree of fluorescence detected in a sample isindicative of the presence of a mismatch between the LNA or PNA probeand the target nucleic acid, such as, in the presence of a mutatedcytosine in a methylated CpG dinucleotide. Preferably, fluorescentlylabelled LNA or PNA technology is used to detect at least a single basechange in a nucleic acid that has been previously amplified using, forexample, an amplification method known in the art and/or describedherein.

As will be apparent to the skilled artisan, LNA or PNA detectiontechnology is amenable to a high-throughput detection of one or moremarkers by immobilizing an LNA or PNA probe to a solid support, asdescribed in Orum et al., Clin. Chem. 45:1898-1905, 1999.

Alternatively, a real-time assay, such as, for example, the so-calledHeavyMethyl assay (Cottrell et al., 2003, supra) is used to determinethe presence or level of methylation of nucleic acid in a test sample.Essentially, this method uses one or more non-extendible nucleic acid(e.g., oligonucleotide) blockers that bind to bisulfite-treated nucleicacid in a methylation specific manner (i.e., the blocker/s bindspecifically to unmutated DNA under moderate to high stringencyconditions). An amplification reaction is performed using one or moreprimers that may optionally be methylation specific but that flank theone or more blockers. In the presence of unmethylated nucleic acid(i.e., non-mutated DNA) the blocker/s bind and no PCR product isproduced. Using a TaqMan assay essentially as described supra the levelof methylation of nucleic acid in a sample is determined.

Other amplification based methods for detecting methylated nucleic acidfollowing treatment with a compound that selectively mutates anon-methylated cytosine residue include, for example,methylation-specific single stranded conformation analysis (MS-SSCA)(Bianco et al., Hum. Mutat., 14:289-293, 1999), methylation-specificdenaturing gradient gel electrophoresis (MS-DGGE) (Abrams and Stanton,Methods Enzymol., 212:71-74, 1992) and methylation-specific denaturinghigh-performance liquid chromatography (MS-DHPLC) (Deng et al. Chin. J.Cancer Res., 12:171-191, 2000). Each of these methods use differenttechniques for detecting nucleic acid differences in an amplificationproduct based on differences in nucleotide sequence and/or secondarystructure. Such methods are clearly contemplated by the presentinvention.

As with other amplification-based assay formats, the amplificationproduct is analyzed using a range of procedures, including gelelectrophoresis, gel filtration, mass spectrometry, and in the case oflabelled primers, by identifying the label in the amplification product.In an alternative embodiment, restriction enzyme digestion of PCRproducts amplified from bisulfite-converted DNA is performed essentiallyas described by Sadri and Hornsby, Nucl. Acids Res. 24:5058-5059, 1996;and Xiong and Laird, Nucl. Acids Res. 25:2532-2534, 1997), to analyzethe product formed.

High throughput detection methods, such as, for example, matrix-assistedlaser desorption/ionization time of flight (MALDI-TOF), electrosprayionization (ESI), Mass spectrometry (including tandem mass spectrometry,e.g. LC MS/MS), biosensor technology, evanescent fiber-optics technologyor DNA chip technology, can also be employed.

As with the other assay formats described herein that utilizehybridization and/or amplification detection systems, combinations ofsuch processes as described herein above are particularly contemplatedby the selective mutagenesis-based assay formats of the presentinvention. In one example, the increased methylation is detected byperforming a process comprising:

(i) treating the nucleic acid with an amount of a compound thatselectively mutates a non-methylated cytosine residue within a CpGdinucleotide under conditions sufficient to induce mutagenesis therebyproducing a mutated nucleic acid;

(ii) hybridizing the nucleic acid to two non-overlapping andnon-complementary primers each of which comprises a nucleotide sequencethat is complementary to a sequence in the DNA comprising a methylatedcytosine residue under conditions such that hybridization to thenon-mutated nucleic acid occurs;

(iii) amplifying nucleic acid intervening the hybridized primers therebyproducing a DNA fragment consisting of a sequence that comprises aprimer sequence;

(iv) hybridizing the amplified DNA fragment to a probe comprising anucleotide sequence that corresponds or is complementary to a sequencecomprising a methylated cytosine residue under conditions such thathybridization to the non-mutated nucleic acid occurs; and detecting thehybridization.

Negative Read-Out Assays

In another example, the assay format comprises a negative read-outsystem in which reduced methylation of DNA from a healthy/normal controlsample is detected as a positive signal and preferably, methylated DNAfrom a neoplastic sample is not detected or is only weakly detected.

In a preferred embodiment, the reduced methylation is determined using aprocess comprising:

(i) treating the nucleic acid with an amount of a compound thatselectively mutates a non-methylated cytosine residue within a CpGisland under conditions sufficient to induce mutagenesis therebyproducing a mutated nucleic acid;

(ii) hybridizing the nucleic acid to a probe or primer comprising anucleotide sequence that is complementary to a sequence comprising themutated cytosine residue under conditions such that selectivehybridization to the mutated nucleic acid occurs; and

(iii) detecting the selective hybridization.

In this context, the term “selective hybridization” means thathybridization of a probe or primer to the mutated nucleic acid occurs ata higher frequency or rate, or has a higher maximum reaction velocity,than hybridization of the same probe or primer to the correspondingnon-mutated sequence. Preferably, the probe or primer does not hybridizeto the methylated sequence (or non-mutated sequence) under the reactionconditions used.

Hybridization-Based Assay Format

In one embodiment the hybridization is detected using Southern, dotblot, slot blot or other nucleic acid hybridization means (Kawai et al.,1994, supra; Gonzalgo et al., 1997, supra). Subject to appropriate probeselection, such assay formats are generally described herein above andapply mutatis mutandis to the presently described selective mutagenesisapproach. Preferably, a ligase chain reaction format is employed todistinguish between a non-mutated and mutated nucleic acid. In thisrespect, the assay requirements and conditions are as described hereinabove for positive read-out assays and apply mutatis mutandis to thepresent format. However the selection of probes will differ. Fornegative read-out assays, one or more probes are selected thatselectively hybridize to the mutated sequence rather than thenon-mutated sequence.

Preferably, the ligase chain reaction probe(s) have 3′-terminal and/or5′-terminal sequences that comprise a CpG dinucleotide that is notmethylated in a healthy control sample, but is hypermethylated incancer, such that the diagnostic probe and contiguous probe are capableof being ligated only when the cytosine of the CpG dinucleotide ismutated to thymidine e.g., in the case of a non-methylated cytosineresidue.

As will be apparent to the skilled artisan the MSO method describedsupra is amenable to either or both positive and/or negative readoutassays. This is because the assay described detects both mutated andnon-mutated sequences thereby facilitating determining the level ofmethylation. However, an assay detecting only methylated ornon-methylated sequences is contemplated by the invention.

Amplification-Based Assay Format

In an alternative example, the hybridization is detected using anamplification system using any amplification assay format as describedherein above for positive read-out assay albeit using primers (andprobes where applicable) selectively hybridize to a mutated nucleicacid.

In adapting the HeavyMethyl assay described supra to a negative read-outformat, the blockers that bind to bisulfite-treated nucleic acid in amethylation specific manner bind specifically to mutated DNA undermoderate to high stringency conditions. An amplification reaction isperformed using one or more primers that may optionally be methylationspecific (i.e. only bind to mutated nucleic acid) but that flank the oneor more blockers. In the presence of methylated nucleic acid (i.e.,mutated DNA) the blocker/s bind and no PCR product is produced.

In one example, the reduced methylation in the normal/healthy controlsubject is detected by performing a process comprising:

(i) treating the nucleic acid with an amount of a compound thatselectively mutates non-methylated cytosine residues under conditionssufficient to induce mutagenesis thereby producing a mutated nucleicacid;

(ii) hybridizing the nucleic acid to two non-overlapping andnon-complementary primers each of which comprises a nucleotide sequencethat is complementary to a sequence in the DNA comprising a mutatedcytosine residue under conditions such that hybridization to the mutatednucleic acid occurs;

(iii) amplifying nucleic acid intervening the hybridized primers therebyproducing a DNA fragment consisting of a sequence that comprises aprimer sequence;

(iv) hybridizing the amplified DNA fragment to a probe comprising anucleotide sequence that corresponds or is complementary to a sequencecomprising a mutated cytosine residue under conditions such thathybridization to the mutated nucleic acid occurs; and

(v) detecting the hybridization.

As will be apparent to the skilled artisan, a negative read-out assaypreferably includes a suitable control sample to ensure that thenegative result is caused by methylated nucleic acid rather than areaction failing.

This invention also provides kits for the detection and/orquantification of the diagnostic sequences of the invention, orexpression or methylation thereof using the methods described herein.

For kits for detection of methylation, the kits of the invention cancomprise at least one polynucleotide that hybridizes to at least one ofthe diagnostic sequences of the invention and at least one reagent fordetection of gene methylation. Reagents for detection of methylationinclude, e.g., sodium bisulfite, polynucleotides designed to hybridizeto sequence that is the product of a biomarker sequence of the inventionif the biomarker sequence is not methylated (e.g., containing at leastone C→U conversion), and/or a methylation-sensitive ormethylation-dependent restriction enzyme. The kits may also includecontrol natural or synthetic DNA sequences representing methylated orunmethylated forms of the sequence. The kits can provide solid supportsin the form of an assay apparatus that is adapted to use in the assay.The kits may further comprise detectable labels, optionally linked to apolynucleotide, e.g., a probe, in the kit. Other materials useful in theperformance of the assays can also be included in the kits, includingtest tubes, transfer pipettes, and the like. The kits can also includewritten instructions for the use of one or more of these reagents in anyof the assays described herein.

The present invention is further described by reference to the followingnon-limiting examples.

Examples Materials and Methods Specimen Collection

Tissue DNA samples were acquired through a commercial specimen bank(BioServe, @, US) and a tertiary referral hospital tissue bank inAdelaide, Australia. Blood plasma specimens were acquired from acommercial specimen bank (Proteogenex, Culver City, Calif.) and atertiary referral hospital in Adelaide, Australia. Blood specimens wereclassified as normal, adenoma or cancer based on colonoscopy resultsverified (where appropriate) by histopathology. This also identified thestage of the cancer. Peripheral blood was drawn into K₃EDTA VACUETTEblood tubes (Greiner-One, Monroe, N.C.) and transported to theprocessing laboratory on wet ice. Whole blood was centrifuged at 1,500 g(4° C.) for 10 minutes within 4 hours of blood draw and plasma wascollected. The plasma was centrifuged for a second time at 1,500 g (4°C.) for 10 minutes, where after the plasma was collected and stored at−80° C. until further use.

Tissue DNA Extraction & Bisulfite Conversion

Tissue specimens were homogenised using a bead homogeniser and genomicDNA extracted using a Wizard® Genomic DNA Purification Kit (Promega,Sydney, Australia).

Commercially acquired DNA was extracted by BioServe (MD, USA). DNAconcentration was determined by Nanodrop ND 1000 20 spectrophometor(Nanodrop Technologies, Wilmington, Del.). The EZ DNA Methylation-GoldKit (Zymo Research Corporation, Orange, Calif. USA) was used forbisulfite conversion of 1 μg of tissue-extracted DNA in accordance withthe manufacturers instructions with the following modification to thebisulfite reaction cycling conditions: 99° C. for 5 minutes, 60° C. for25 minutes, 99° C. for 5 minutes, 60° C. for 85 minutes, 99° C. for 5minutes and 60° C. for 175 minutes. The concentration of purifiedbisulfite converted DNA was determined by qPCR using bisulfiteconversion specific primers to beta-Actin [ACTB1] as described in Table1 and previously by Devos et al. (Clin. Chem., 2009; 55(7):1337-1346).The bisulfite converted DNA samples were stored at −80° C. until furtheruse.

Plasma DNA Extraction & Bisulfite Conversion:

DNA was prepared from 4 mL of plasma using the QIAamp CirculatingNucleic Acid Kit (QIAGEN, Dusseldorf, Germany) according to themanufacturer's specifications with the following modifications: Thecolumn was washed twice with 750 ul of ACW2 and twice with 750 ul ofabsolute ethanol (200 proof). The resulting DNA was eluted in 35 ul ofbuffer AVE and this eluate was then reapplied to the column and elutedagain to increase the concentration of the DNA. The optimised protocolresulted in a 20% improvement in DNA yield compared to the recommendedmanufacturer protocol (data not shown). The final volume of plasma DNAwas ˜324 per 4 mL of patient plasma. Real-time PCR was used to measurethe total DNA recovery: 2×14 aliquots of the resulting plasma DNA wasused in a previously described CFF1 assay (Devos et al. 2009. Clin Chem)(Table 1).

All PCRs were performed on the LightCycler 480 Real-Time PCR System,model II (Roche). A 4-fold serial dilution of sonicated genomic bloodDNA (Roche, Mannheim, Germany) was used as a standard to determine theamount (ng) of DNA extracted per mL of plasma 304 of DNA extracted from4 mL plasma was stripped of DNA-binding proteins by incubation at 37° C.for 1 hour after adding 3 uL of a Lysis Buffer consisting of 1 mg/mLtRNA, 2 mg/mL Proteinase K and 10% SDS. The samples were subsequentlybisulphite converted using either the EZ DNA Methylation-Gold Kit™ asrecommended by the manufacturer (Zymo Research Corp. Orange, Calif.USA), with the same modification to thermal cycling conditions describedabove, or the Epitect Plus DNA Bisulfite Kit using Epitect Fastbisulfite reagent (QIAGEN, Dusseldorf, Germany) using conditionsrecommended by the manufacturer. In both cases, the purified DNA waseluted with 40 uL nuclease-free water. The resulting bisulphite DNAconcentration was calculated by analysing 24 in the ACTB PCR assay asdescribed above. Triplicate 5 uL aliquots of the resulting 36 uLbisulphite converted DNA extracted from 4 mL plasma (the equivalent of5554 plasma per aliquot) were analysed in methylation-specific qPCRassays as described below.

Measurement of Methylation

Methylation specific oligonucleotide primers and probes were designed tointerrogate the methylation status of sites within CAHM, GRASP, IRF4,BCAT1 and IKZF1. PCR was performed in triplicate on bisulfite-convertedtissue DNA (5 ng) or 54 plasma DNA in a total volume of 154 (see Table 1for primer/probe sequences and reaction conditions). Melt peaks of78.4°+/−0.9° C. (CAHM) and 82.9.4°+/−0.3° C. (IKZF1) were characteristicfor the amplicons which ran without a probe. Methylation levels werequantified against an in house made standard curve consisting of aserial dilution of bisulfite-converted sheared methylated DNA (CpGenomeUniversal Methylated DNA, Chemicon, Temecula, Calif., USA) in abackground of sheared bisulfite-converted white blood cell DNA (Roche,Mannheim, Germany). The standard curve contained the following dilutionpoints: 5000-, 1250-, 312.5-, 78.125, 19.53-, 4.88-, 1.22- and 0 pg mCpGin a background of WBC DNA (5 ng total DNA per reaction).

Estimation of Class Probabilities

The R open source programming language and environment for statisticalcomputing and graphics (http://www.r-project.org) was installed on astandard Intel IA-32 personal computer system and used to access andprocess input data representing the measured methylation levels andcorresponding observed non-neoplastic and neoplastic categories, asdescribed below.

Specifically, the observed methylated CAHM mass by phenotypeclassification (FIG. 1B) was used to determine the empirical probabilitydensity plots for phenotype classes (premalignant, early stage cancer,late stage cancer) (FIG. 3A), and the estimated means and standarddeviation values were then used to generate the modelled density plotsof FIG. 3B assuming the observed methylation levels are drawn from anormal distribution. The density distributions were then used toestimate the probability that an assayed CAHM methylation level for apatient specimen is drawn from one of these classifications.

Using only positive (i.e., greater than zero)_methylation levelsdetermined for plasma specimens of known phenotype (and shown in FIG.1B), the corresponding estimated distribution profiles are shown in FIG.3B. These density functions were used to calculate the relativeprobability that a plasma specimen with a methylated CAHM level of 2.8pg, 148 pg or 22,000 pg is likely to be drawn from a patient diagnosedwith colorectal lesions classified as pre-malignant (i.e., adenoma),early-stage cancer (Stage 1 or Stage 2), or late stage cancer (Stage 3or Stage 4).

RELATIVE Probability (normalised to premalignant) Early-Stage Late-StageLog(methyl CAHM pg) Premalignant Cancer Cancer 1.0 (2.8 pg) 1.0 1.00.175 5.0 (148 pg) 1.0 3.2 4.95 10.0 (22,000 pg) 1.0 8.3 627

These data were also used to estimate the probability that a plasmaspecimen from a known classification would yield an observed methylationlevel equal to or greater than the hypothetical CAHM methylation levels.Using the probability density functions shown in FIG. 3B and determinedfrom the raw CAHM methylation levels shown in FIG. 1B, it was determinedthat only 3.0% of premalignant plasma specimens are found to contain atleast 148 pg methylated CAHM, while 66% late stage cancers show 148 pgmethylation or more (relative value of 23:1). Further, a plasma specimenyielding 22 ng of methylated CAHM is approximately 1600 times morelikely to be drawn from a patient with late cancer than a patient with apremalignant neoplasm.

Cumulative probability methylated CAHM is greater than or equal to(ratio to premalignant) Log(methyl Early-Stage Late-Stage CAHM pg)Premalignant Cancer Cancer 1.0 36% (1.0) 68% (1.8) 96% (2.6) 5.0 3%(1.0) 12% (4.1) 66% (23.2) 10.0 0.0058% (1.0) 0.052% (8) 9% (1600)

Those skilled in the art will appreciate that the invention describedherein is susceptible to variations and modifications other than thosespecifically described. It is to be understood that the inventionincludes all such variations and modifications. The invention alsoincludes all of the steps, features, compositions and compounds referredto or indicated in this specification, individually or collectively, andany and all combinations of any two or more of said steps or features.

TABLE 1Oligonucleotide sequences and reaction conditions for PCR, Methylation SpecificPCR and Methylight assays. PCR Primer/Probe Sequence MastermixCycling Conditions CAHM Forward: GAAGGAAGTATEach 15 μL reaction contained: Activation - 95° C. 2 min.TTCGAGTACGATTGAC 0.1 μL 5 U/μL Platinum Taq DNA 3 Cycles: 92° C. 15 secReverse: CCCGAACGCAA polymerase (Invitrogen), 1.5 μL(4.4° C./sec), 62° C. 15 sec CGACTTAA 10X Platinum Buffer (Invitrogen),(2.2° C./sec), 72° C. 20 sec 0.9 μL 50 mM MgCl₂ (f 3 mM Final,50 Cycles: 82° C. 15 sec Invitrogen), 0.3 μL 10 mM dNTPs(4.4° C./sec), 63° C. 15 sec (200 uM Final, Promega), 0.1 μL of(2.2° C./sec), 72° C. 20 sec the forward and reverse primersCooling - 40° C. 5 sec (50 uM/200 nM Final) and 0.125 μL(2.2° C./sec) followed by a 1/1000 SYBR Green and NucleaseMelt analysis to confirm Free Water correct product GRASP Forward:Each 15 μL reaction contained: Activation - 95° C. 2 min.CGGAAGTCGCGTTCGT 0.1 μL 5 U/μL Platinum Taq DNA 3 Cycles: 92° C. 15 secC polymerase (Invitrogen), 1.5 μL (4.4° C./sec), 64° C. 15 sec Reverse:10X Platinum Buffer (Invitrogen), (2.2° C./sec), 72° C. 20 secGCGTACAACTCGTCCG 1.2 μL 50 mM MgCl₂ (4 mM Final, (4.4° C./sec) CTAAInvitrogen), 0.3 μL 10 mM dNTPs 47 Cycles: 85° C. 15 sec Probe: [HEX](0.2 mM Final, Promega), 0.06 μL (4.4° C./sec), 64° C. 15 secTTCGATTTCGGGATTTT of the forward and reverse primers(2.2° C./sec), 72° C. 20 sec TTGTCGTAGTC[BHQ1](50 uM/200 nM Final) and 0.03 μL of (4.4° C./sec)probe (50 uM stock/100 nM Final) cooling - 40° C. 10 sec (2.2° C./sec).IRF4 Forward: Each 15 μL reaction contained: Activation - 95° C. 2 min.TGGGTGTTTTGGACGGT 0.1 μL 5 U/μL Platinum Taq DNA 3 Cycles: 95° C. 15 secTTC polymerase (Invitrogen), 1.5 μL (4.4° C./sec), 64° C. 30 secReverse: 10X Platinum Buffer (Invitrogen), (2.2° C./sec), 72° C. 30 secCGCCTACCCTCCGCG 1.2 μL 50 mM MgCl₂ (4 mM Final, (4.4° C./sec)Probe: [HEX] Invitrogen), 0.3 μL 10 mM dNTPs 50 Cycles: 86° C. 15 secTCGTTTAGTTTGTGGCG (0.2 mM Final, Promega), 0.12 μL(4.4° C./sec), 62° C. 30 sec ATTTCGTCG {BHQ1]of the forward and reverse primers (2.2° C./sec), 72° C. 30 sec(50 uM/400 nM Final) and 0.3 ul of (4.4° C./sec)probe (10 uM stock/200 nM Final) cooling - 40° C. 10 sec (2.2° C./sec).BCAT1 Forward: Each 15 μL reaction contained: Activation - 95° C. 2 min.GTTTTTTTGTTGATGTA 0.1 μL 5 U/μL Platinum Taq DNA50 Cycles: 95° C. 15 sec ATTCGTTAGGTC polymerase (Invitrogen), 1.5 μL(4.4° C./sec), 62° C. 30 sec Reverse: 10X Platinum Buffer (Invitrogen),(2.2° C./sec), 72° C. 30 sec CAATACCCGAAACGAC1.2 μL 50 mM MgCl₂ (4 mM Final, (4.4° C./sec) GACGInvitrogen), 0.3 μL 10 mM dNTPs cooling - 40° C. 5 sec Probe: HEX-5′(0.2 mM Final, Promega), 0.06 μL (2.2° C./sec). TTCGTCGCGAGAGGGTof the forward and reverse primers CGGTT -BHQ(50 uM/200 nM Final) and 0.15 uL of probe (10 uM stock/100 nM Final)IKZF1 Forward: Each 15 μL reaction contained: Activation - 95° C. 2 min.GACGACGTATTTTTTTC 7.5 ul of 2x GoTaq Hot Start buffer50 Cycles: 95° C. 15 sec GTGTTTC w/MgCL2, 0.3 μL 50 mM MgCl₂(4.4° C./sec), 62° C. 30 sec Reverse: (4 mM Final, Invitrogen), 0.06 μL(2.2° C./sec), 72° C. 30 sec GCGCACCTCTCGACCGof the forward and reverse primers (4.4° C./sec)(50 uM/200 nM Final) and 0.15 ul of cooling - 40° C. 5 secSYBR (1:1000 stock/1:100,000 (2.2° C./sec). Final) CFF1Forward: TAAGAGTAATA Each 15 μL reaction contained:Activation - 95° C. 2 min. ATGGATGGATGATG0.15 μL 5 U/μL Platinum Taq DNA 50 Cycles: 95° C. 10 sec Reverse:polymerase (Invitrogen), 1.5 μL (4.4° C./sec), 58° C. 60 secCCTCCCATCTCCCTTCC 10X Platinum Buffer (Invitrogen), (2.2° C./sec)Probe: 6FAM- 0.9 μL 50 mM MgCl₂ (3 mM Final, cooling - 40° C. 5 secATGGATGAAGAAAGAA Invitrogen), 0.3 μL 10 mM dNTPs (2.2° C./sec).AGGATGAGT-BHQ-1 (0.2 mM Final, Promega), 0.189 μLof the forward and reverse primers (50 uM/200 nM Final) and 0.3 ul ofprobe (10 uM stock/200 nM Final) β-actin Forward: GTGATGGAGGAEach 15 μL reaction contained: Activation - 95° C. 2 min. GGTTTAGTAAGTT0.15 μL 5 U/μL Platinum Taq DNA 60 Cycles: 95° C. 10 secReverse: CCAATAAAACC polymerase (Invitrogen), 1.5 μL(4.4° C./sec), 57° C. 40 sec TACTCCTCCCTTAA10X Platinum Buffer (Invitrogen), (2.2° C./sec), 72° C. l0 secProbe: FAM- 0.6 μL 50 mM MgCl₂ (2 mM Final, (4.4° C./sec)ACCACCACCCAACACA Invitrogen), 0.3 μL 10 mM dNTPs cooling - 40° C. 5 secCAATAACAAACACA- (0.2 mM Final, Promega), 0.27 μL (2.2° C./sec). BHQ1of the forward and reverse primers (50 uM/900 nM Final) and 0.15 ul ofprobe (10 uM stock/100 nM Final)

TABLE 2 Coordinates Oligonucleotide sequences GenomicCurrent sub-region(s) of interest (genomic of sub-Resulting bisulphite converted sequence for measurement of Gene Strandsequence) region(s) (strands no longer complementary) methylation levelsBCAT1 top 5′-cagtgccCGaggCGgCGgCGagtacaCGtggC 25,101,992-5′-tagtgttCGaggCGgCGgCGagtataCGtggCGggttgga strandGggctggattgcagacCGgccctctCGCGgCGgagactCGC 25,102,093ttgtagatCGgttttttCGCGgCGgagattCGCGatttagCGgattGacctagCGgattgcatcagcaggaagac (SEQ ID No: 1) gtattagtaggaagat minus3′-gtcacggGCtccGCcGCcGCtcatgtGCaccGCc3′-gttatggGCtttGCtGCtGCttatgtGCattGCttgatttaatg5′-gtttttttgttgatgtaattcgtt strandcgacctaacgtctgGCcgggagaGCGCcGCctctgaGCGCttttgGCtgggagaGCGCtGCttttgaGCGCtggattGCttaatgt aggtcggatcGCctaacgtagtcgtccttctg agttgtttttttg 5′-caatacccgaaacgacgacg5′-ttcgtcgcgagagggtcggtt 5′-tttttgttgatgtaattcgttagg tc5′-attacaaaccgaccctctcg top 5′-agatcccaagggtCGtagcccctggcCGtgtggacCGg25,101,909- This sequence is for measuring CpG methylation5′-agatcccaagggtcgtagc strandgtctgCGgctgcagagCGCGgtccCGgctgcagcaagacctgg 25,101,995levels using methylation sensitive restriction 5′-actgccccaggtcttgctggcagt ((SEQ ID No: 2) enzymes (e.g. HbaII, HhaI (underlined) minus3′-tctagggttcccaGCatcggggaccgGCacacctgGCc strandcagacGCcgacgtctcGCGCcaggGCcgacgtcgttctggacc ccgtca IKZF1 top5′-gaCGaCGcaccctctcCGtgtccCGctctgCGccctt 50,343,867-5′-gaCGaCGtatttttttCGtgtttCGttttgCGtttttttgCGCG5′-gacgacgtatttttttcgtgtttc strandctgCGCGcccCGctccctgtacCGgagcagCGatcCGggag 50,343,961tttCGttttttgtatCGgagtagCGattCGggaggCGgtCGagagg 5′-gcgcacctctcgaccggCGgcCGagaggtgCGc (SEQ ID No: 3) tgCGt 5′-tttgtatcggagtagcgattcggg agminus 3′-ctGCtGCgtgggagagGCacaggGCgagacGCgg3′-ttGCtGCgtgggagagGCataggGCgagatGCgggaa strandgaagacGCGCgggGCgagggacatgGCctcgtcGCtagGCgatGCGCgggGCgagggatatgGCtttgttGCtagGCtttttGCt cctccGCcgGCtctccacGCggGCtttttatGCg top 5′-cCGgagttgCGgctgagaCGCGCGcCGCGCG 50,343,804-This sequence is for measuring CpG methylation 5′-ggagttgcggctgagacstrand agcCGggggactCGgCGaCGgggCGgggaCGggaCGa 50,343,895levels using methylation sensitive restriction 5′-agagcgggacacggagaCGcaccctctcCGtgtccCGctct (SEQ ID No: 4)enzymes (e.g. HbaII, HhaI (underlined) minus3′-gGCctcaacGCcgactctGCGCGCgGCGCGC strandtcgGCcccctgaGCcGCtGCcccGCccctGCcctGCtGC gtgggagagGCacaggGCgaga IRF4 top5′-CGcctgccctcCGCGctcctgCGaCGgggtCGcc 392,036-5′-CGtttgtttttCGCGtttttgCGaCGgggtCGttataagttg 5′- gtttttgcgacggggtcstrand acaagctggaCGggatgagctaacCGgactgtCGgggccccag 392,145gaCGggatgagttaatCGgattgtCGgggttttaggagtggttgagg 5′-taaaaccccgacaatccggagtggctgaggCGgggcCGtccaaggcaccca (SEQ ID CGgggtCGtttaaggtattta No: 5)minus 3′-GCggacgggagGCGCgaggacGCtGCcccaGC3′-GCggatgggagGCGCgaggatGCtGCtttaGCggtgtttg 5′-tgggtgttttggacggtttcstrand ggtgttcgacctGCcctactcgattgGCctgacaGCcccggggtcatttGCtttatttgattgGCttgataGCtttggggtttttattgat5′-tagttatttttggggtttcgatagt ctcaccgactccGCcccgGCaggttccgtgggttttGCtttgGCaggttttgtgggt tc 5′-cgcctaccctccgcg5′-tcgtttagtttgtggcgatttcgt cg GRASP top5′-caggaagctgcagcagaaggaggaggCGgCGgcca 52,400,821-5′-taggaagttgtagtagaaggaggaggCGgCGgttatttCGga 5′-cggaagtcgcgttcgtcstrand cccCGgacccCGcCGccCGgactccCGactCGgaagtCG 52,401,051tttCGtCGttCGgattttCGattCGgaagtCGCGttCGtCGttt 5′-gcgtacaactcgtccgctaaCGccCGcCGctcCGgtccCGacccCGggaccccctgcCGCGgtttCGatttCGggattttttgtCGtagtCGttatttttgggtt5′-ttcgatttcgggattttttgtcgt cagcCGccacccctgggcccccagCGgaCGagctgtaCGCGtttagCGgaCGagttgtaCGCGgCGttggaggattattattttgtCG agtcgCGctggaggactatcaccctgcCGagctgtacCGCGCGctCagttgtatCGCGCGttCGtCGtgttCGggggtattttgtttCGtCGa 5′-cggattttcgattcggaagtGcCGtgtcCGggggcaccctgcccCGcCGaaaggtgCGtccaaggtgCGtttttCGttCGtttttaggatttgtttagttttttttCGccCGccCGccttcaggatctgctcagcccctctcCGactccctacaattttttatagggtttgttgatttCG gggcctgctgactcCG (SEQ ID No: 6) minus3′-gtccttcgacgtcgtcttcctcctccGCcGCcggtgggG3′-gttttttgatgttgttttttttttttGCtGCtggtgggGCttggg 5′-ggtagggtgttttcggatacstrand CctgggGCgGCggGCctgaggGCtgaGCctcaGCGCggGCgGCggGCttgaggGCtgaGCtttaGCGCggGCgGCgagG 5′-aacgaacgaactatacgcgacGCgGCgagGCcaggGCtgggGCcctgggggacgGCgtcgCtaggGCtgggGCtttgggggatgGCgttgGCggtggggatttggGCggtggggacccgggggtcGCctGCtcgacatGCGCcGCgggttGCttGCttgatatGCGCtGCgattttttgatagtgggatgGCgacctcctgatagtgggacgGCtcgacatgGCGCGCgaGCgttgatatgGCGCGCgaGCgGCatagGCttttgtgggatgggGCGCacagGCccccgtgggacgggGCgGCtttccacGCagggggGCtttttatGCaggggGCggGCggaagttttagatgagttggggaGCggGCggaagtcctagacgagtcggggagagGCtgagggatggagGCtgagggatgttttggatgattgagGC tcccggacgactgagGC top5′-gacagagacagccccaggcaagttgaaggtcCGagagc 52,401,407-5′-gatagagatagttttaggtaagttgaaggttCGagagttttCGgt strandcccCGgtgggagaagCGggcCGgtggctgCGcCGCGtgC 52,401,664gggagaagCGggtCGgtggttgCGtCGCGtgCGtttttattttgaggGttctcactctgaggaagtgCGtggggagcCGctgactcCGgataaagtgCGtggggagtCGttgatttCGgatagtatattttttCGagggggcacacccttcCGaggggactcccCGattcctgggctgggggcctatttttCGatttttgggttgggggtttgtCGtttggttttaCGtttgagcCGcctggccccaCGtctgaCGtaCGgggCGCGagggccCGtaCGgggCGCGagggttattgttttttggatttttgtCGgaatCGgactgctccctggacttctgtCGgaacCGgaCGcagtgggaggggt aCGtagtgggaggggtCGtaggCGcagg (SEQ ID No: 7) minus 3′-ctgtctctgtcggggtccgttcaacttccagGCtctcgggg3′-ttgtttttgttggggtttgtttaatttttagGCttttggggGCtat5′-cggagttagcggttttttacg strand GCcaccctcttcGCccgGCcaccgacGCgGCGCacGCaatttttttGCttgGCtattgatGCgGCGCatGCaagagtgagattttttt5′-cgataaaaaaaacgaaccga gagtgagactccttcacGCacccctcgGCgactgagGCctatcgtatGCattttttgGCgattgagGCttattgtgtgggaagGCttttttgag5′-agagtgagaacgtacgcggc gtgggaagGCtcccctgagggGCtaaggacccgacccccggacgggGCtaaggatttgatttttggatgGCggattggggtGCagattGCatGGCggaccggggtGCagactGCatGCcccGCGCtcccggtgCtttGCGCttttggtgatgagggatttgaagataGCtttgGCttGCgttacgagggacctgaagacaGCcttgGCctGCgtcaccctccccaG attttttttaGCgttt Cgtcc top5′-gacagagacagccccaggcaagttgaaggtcCGagagThis sequence is for measuring CpG methylation 5′-caagttgaaggtccgagagcstrand ccccCGgtgggagaagCGggcCGgtggctgCGcCGCGtglevels using methylation sensitive restriction 5′-cgcacttcctcagagtgagaCGttctcactctgaggaagtgCGtggggagcCGctgactcCGgaenzymes (e.g. HbaII, HhaI (underlined)tagcacacccttcCGaggggactcccCGattcctgggctgggggcctgcCGcctggccccaCGtctgaCGtaCGgggCGCGagggccactgctccctggacttctgtCGgaacCGgaCGcagtgggaggg gtCGcagg minus3′-ctgtctctgtcggggtccgttcaacttccagGCtctcgggg strandGCcaccctcttcGCccgGCcaccgacGCgGCGCacGCaagagtgagactccttcacGCacccctcgGCgactgagGCctatcgtgtgggaagGCtcccctgagggGCtaaggacccgacccccggacgGCggaccggggtGCagactGCatGCcccGCGCtcccggtgacgagggacctgaagacaGCcttgGCctGCgtcaccctccccaG Cgtcc CAHM top5′-atctgtaaaaatgttgacttctgcttttcagactaCGCGcac 163,834,2955′-atttgtaaaaatgttgatttttgttttttagattaCGCGtatagtt5′-gaaggaagtatttcgagtacgatt strandagcctctttatttcctactgCGgcttcattccctcaCGgaacactg 163,834,500tttttattttttattgCGgttttatttttttaCGgaatattgaCGttat gaccaCGccatCGCGaaggaagcatttCGagcaCGactgaCGctccccCGCGaaggaagtatttCGagtaCGattgaCGttttttttattatttgtt 5′-cccgaacgcaacgacttaattattatttgctaagcCGctgCGctCGggtctggctaCGatttgctaagtCGttgCGttCGggtttggttaCGatttgtttttagaataaCGgga5′-gcctctaaaaaaacgatcttatta ttcagaataaCGggaaggtgcaacaaga (SEQ ID No: 8)aggtgtaataaga cacc minus 3′-tagacatttttacaactgaagacgaaaagtctgatGCGCg3′-tagatatttttataattgaagatgaaaagtttgatGCGCgtgttgg 5′-gaaacactaacgccatcgstrand tgtcggagaaataaaggatgacGCcgaagtaagggagtGCcttgtgagaaataaaggatgatGCtgaagtaagggagtGCtttgtgattGCggta5′-cgtagttagattcgagcgtag actGCggtaGCGCttccttcgtaaaGCtcgtGCtgactGCgagGCGCtttttttgtaaaGCttgtGCtgattGCgaggggaataataaatg5′-aggggagcgttagtcgtgttcg gggaataataaacgattcgGCgacGCgaGCccagaccgatGCtatttgGCgatGCgaGCttagattgatGCtaaatgaaagttttattGCtt aaaaaacgaaagtcttattGCccttccacgttgact ttttatgttgtttt minus3′-cgGCacgacgaaaggtcggagagtcgtttagtGCttgt 163,834,621tgGCatgatgaaaggttggagagttgtttagtGCttgtgGCtttttttg5′-gtttttttcggcgataaagc strand gGCtttcttcggtGCcGCcGCtGCcctccccGCaGCGCG163,834,906 gtGCtGCtGCtGCtttttttGCaGCGCGCatgaagggaGCtGC5′-cgcctctacgaaactctacg CacgaagggaGCcGCtgtttcGCcctcgGCccGCGCgGCtgttttGCttttgGCttGCGCgGCtgGCttttGCggGCtGCgttt 5′-cgtcggtcgagggcgttccgGCtcccGCggGCcGCgtctcaggGCgtctccGCctGCgtaggGCgtttttGCttGCgGCGCtgtGCGCggaGCtttttggagGCGCcgtGCGCggaGCttttcggagtttgagaataggaGCcgtttgagaataggaGCtgagaggGCggggtggagGCgggGCgttgagaggGCggggtggagGCgggGCgtcggttctggGCGCgGgttttggGCGCgGCattGCttggGCtGCtggttttttttgggtggttgCaccGCccggGCtGCcggttcctttcgggtggtcgggagGC ggagGC tgGCat tgGCac

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1. (canceled)
 2. A method comprising measuring a methylation level of a DNA region of a sample from an individual having or suspected of having a large intestine neoplasm, wherein said measuring of a methylation level of a DNA region of a sample from said individual comprises: selecting an individual from a patient population known or suspected to have a large intestine neoplasm staged as adenoma, stage I, stage II, stage III, or stage IV; obtaining or having obtained a blood-derived sample from said individual, the blood-derived sample comprising circulating cell-free DNA; extracting circulating cell-free DNA from the sample; bisulfite converting the circulating cell-free DNA; and detecting a level of methylation of a DNA region of the bisulfite converted DNA, wherein said detecting comprises hybridizing methylation-specific oligonucleotide primers to the DNA region of the bisulfite converted DNA, wherein the DNA region comprises: (i) the region, including 2 kb upstream of the transcription start site, defined by chr7:50344378..50472798 and at least one of Hg19 coordinates: (1) chr12:24962958..25102393; (2) chr6:391739..411443; (3) chr12:52400748..52409671; or (4) chr6:163834097..163834982; or (ii) the gene region, including 2 kb upstream of IKZF1 and at least one of: (1) BCAT1; (2) IRF4; (3) GRASP; or (4) CAHM; determining a probability whether said individual has a premalignant neoplasm, an early stage malignant neoplasm or a late stage malignant neoplasm from said measurement of said methylation level of said DNA region of said sample from said individual.
 3. The method of claim 2, wherein said methylation level is measured in (1) IKZF1 subregions: chr7:50343867-50343961 (SEQ ID NO: 3 or corresponding minus strand) and chr7:50343804-5033895 (SEQ ID NO: 4 or corresponding minus strand), and one or more chromosomal subregions selected from: (2) BCAT1 subregions chr12:25101992-25102093 (SEQ ID NO: 1 or corresponding minus strand) and chr12:25101909-25101995 (SEQ ID NO: 2 or corresponding minus strand) (3) IRF4 subregions chr6:392036-392145 (SEQ ID NO: 5 or corresponding minus strand) (4) GRASP subregions: chr12:52399672-52399922, chr12:52400821-52401051 (SEQ ID NO: 6 or corresponding minus strand), chr12:52401407-52401664 (SEQ ID NO: 7 or corresponding minus strand) chr12:52400866-52400973 and Chr12:52401107-52401664, or (5) CAHM subregions: chr6:163834295-163834500 (SEQ ID NO: 8 or corresponding minus strand), chr6:163834621-163834906, chr6:163834393-163834455 and chr6: 163834393-163834519.
 4. The method of claim 3, wherein said subregion is selected from SEQ ID NO: 1 or SEQ ID NO: 2, and SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, or SEQ ID NO: 8 or corresponding minus strands.
 5. The method of claim 3, said method comprising measuring the methylation of one or more cytosine residues selected from: (IKZF1) chr7: 50343869 chr7: 50343872 chr7: 50343883 chr7: 50343889 chr7: 50343890 chr7: 50343897 chr7: 50343907 chr7: 50343909 chr7: 50343914 chr7: 50343934 chr7: 50343939 chr7: 50343950 chr7: 50343959 chr7: 50343805 chr7: 50343822 chr7: 50343824 chr7: 50343826 chr7: 50343829 chr7: 50343831 chr7: 50343833 chr7: 50343838 chr7: 50343847 chr7: 50343850 chr7: 50343858 chr7: 50343864 chr7: 50343869 chr7: 50343872 chr7: 50343890 (BCAT1) chr12: 25101998 chr12: 25102003 chr12: 25102006 chr12: 25102009 chr12: 25102017 chr12: 25102022 chr12: 25102039 chr12: 25102048 chr12: 25102050 chr12: 25102053 chr12: 25102061 chr12: 25102063 chr12: 25102071 chrl12: 25101921 chr12: 25101934 chr12: 25101943 chr12: 25101951 chr12: 25101962 chr12: 25101964 chr12: 25101970 (GRASP) chr12: 52399713 chr12: 52399731 chr12: 52399749 chr12: 52399783 chr12: 52399796 chr12: 52399808 chr12: 52399823 chr12: 52399835 chr12: 52399891 chr12: 52400847 chr12: 52400850 chr12: 52400859 chr12: 52400866 chr12: 52400869 chr12: 52400873 chr12: 52400881 chr12: 52400886 chr12: 52400893 chr12: 52400895 chr12: 52400899 chr12: 52400902 chr12: 52400907 chr12: 52400913 chr12: 52400919 chr12: 52400932 chr12: 52400938 chr12: 52400958 chr12: 52400962 chr12: 52400971 chr12: 52400973 chr12: 52400976 chr12: 52400998 chr12: 52401008 chr12: 52401010 chr12: 52401012 chr12: 52401016 chr12: 52401019 chr12: 52401025 chr12: 52401041 chr12: 52401044 chr12: 52401053 chr12: 52401060 chr12: 52401064 chr12: 52401092 chr12: 52401118 chr12: 52401438 chr12: 52401448 chr12: 52401460 chr12: 52401465 chr12: 52401474 chr12: 52401477 chr12: 52401479 chr12: 52401483 chr12: 52401504 chr12: 52401514 chr12: 52401523 chr12: 52401540 chr12: 52401553 chr12: 52401576 chr12: 52401588 chr12: 52401595 chr12: 52401599 chr12: 52401604 chr12: 52401606 chr12: 52401634 chr12: 52401640 chr12: 52401644 chr12: 52401659 chr12: 52401160 chr12: 52401165 chr12: 52401174 chr12: 52401177 chr12: 52401179 chr12: 52401183 chr12: 52401204 chr12: 52401215 chr12: 52401223 chr12: 52401240 chr12: 52401253 chr12: 52401288 chr12: 52401295 chr12: 52401299 chr12: 52401304 chr12: 52401334 chr12: 52401340 chr12: 52401344 chr12: 52401359 (CAHM) chr6: 163834330 chr6: 163834332 chr6: 163834357 chr6: 163834373 chr6: 163834384 chr6: 163834390 chr6: 163834392 chr6: 163834406 chr6: 163834412 chr6: 163834419 chr6: 163834443 chr6: 163834448 chr6: 163834452 chr6: 163834464 chr6: 163834483 chr6: 163834653 chr6: 163834660 chr6: 163834672 chr6: 163834675 chr6: 163834678 chr6: 163834681 chr6: 163834815 chr6: 163834824 chr6: 163834835 chr6: 163834840 chr6: 163834853 chr6: 163834855 chr6: 163834858 chr6: 163834863 chr6: 163834869 chr6: 163834872 (IRF4) chr6: 392036 chr6: 392047 chr6: 392049 chr6: 392057 chr6: 392060 chr6: 392066 chr6: 392080 chr6: 392094 chr6: 392102 chr6: 392131

or a corresponding cytosine at position n+1 on the opposite DNA strand.
 6. The method of claim 2, wherein any one of said DNA regions exhibit a higher level of methylation relative to a control sample.
 7. The method of claim 2, wherein any two or more of said DNA regions exhibits a higher level of methylation relative to a control sample.
 8. The method of claim 2, wherein said neoplasm is an adenoma or an adenocarcinoma.
 9. The method of claim 2, wherein said neoplasm is a colorectal neoplasm.
 10. The method of claim 2, wherein said level of methylation is used to determine one or more probabilities of respective classifications of said large intestine neoplasm of said individual into one or more neoplastic categories selected from adenoma, stage I, stage II, stage III, or stage IV categories.
 11. The method of claim 10, wherein said level of methylation is used to determine one or more probabilities of respective classifications of said large intestine neoplasm of said individual into one or more aggregates of fewer than five of said neoplastic categories.
 12. The method of claim 2, wherein said level of methylation is used to determine a probability that said large intestine of said individual would be classified as non-neoplastic, based on comparison of said level of methylation relative to said corresponding measured levels of methylation and to corresponding measured levels of methylation from a population of individuals whose large intestines were classified as non-neoplastic.
 13. The method of claim 11, wherein said aggregates include one or more of: (i) one or more aggregates of fewer than five of said neoplastic categories and an aggregate of the non-neoplastic category with at least the adenoma category; (ii) a pre-malignant neoplasm category consisting of an aggregate of the non-neoplastic and adenoma categories; (iii) an early stage malignant neoplasm category consisting of an aggregate of the stage I and stage II categories; (iv) a late stage malignant neoplasm category consisting of an aggregate of the stage III and stage IV categories; or (v) the pre-malignant neoplasm category, the early stage malignant neoplasm category, and the late stage malignant neoplasm category. 